Variant report

Variant	rs2526396
Chromosome Location	chr3:50188309-50188310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:50188137-50188628	T-47D	breast:	n/a	n/a
2	STAT3	chr3:50188173-50188591	MCF10A-Er-Src	breast:	n/a	chr3:50188359-50188371 chr3:50188476-50188488
3	EP300	chr3:50188124-50188656	T-47D	breast:	n/a	n/a
4	STAT3	chr3:50188084-50188554	MCF10A-Er-Src	breast:	n/a	chr3:50188359-50188371 chr3:50188476-50188488
5	HDAC2	chr3:50188086-50188756	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr3:50187906-50189017	MCF-7	breast:	n/a	n/a
7	ESR1	chr3:50188147-50188724	T-47D	breast:	n/a	n/a
8	NR2F2	chr3:50187971-50189510	MCF-7	breast:	n/a	n/a
9	ESR1	chr3:50188130-50188731	T-47D	breast:	n/a	n/a
10	MAX	chr3:50187903-50189071	MCF-7	breast:	n/a	chr3:50188480-50188490
11	ESR1	chr3:50188177-50188514	T-47D	breast:	n/a	n/a
12	GATA3	chr3:50188149-50188426	SH-SY5Y	brain:	n/a	n/a
13	GATA2	chr3:50188159-50188586	SH-SY5Y	brain:	n/a	n/a
14	MYC	chr3:50188265-50188426	MCF-7	breast:	n/a	n/a
15	NR2F2	chr3:50188015-50189077	MCF-7	breast:	n/a	n/a
16	ESR1	chr3:50188068-50188742	T-47D	breast:	n/a	n/a
17	STAT3	chr3:50188066-50188474	MCF10A-Er-Src	breast:	n/a	chr3:50188359-50188371
18	GATA3	chr3:50187904-50188899	MCF-7	breast:	n/a	n/a
19	MYC	chr3:50188035-50188716	MCF10A-Er-Src	breast:	n/a	chr3:50188480-50188490
20	FOXM1	chr3:50188076-50188800	MCF-7	breast:	n/a	n/a
21	EP300	chr3:50188085-50188864	T-47D	breast:	n/a	n/a
22	FOS	chr3:50188274-50188388	MCF10A-Er-Src	breast:	n/a	n/a
23	ESR1	chr3:50188123-50188563	T-47D	breast:	n/a	n/a
24	GATA3	chr3:50187965-50188709	T-47D	breast:	n/a	n/a
25	ZNF217	chr3:50188018-50189463	MCF-7	breast:	n/a	n/a
26	HDAC2	chr3:50188101-50188705	MCF-7	breast:	n/a	n/a
27	FOS	chr3:50188264-50188662	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr3:50187858-50188622	MCF10A-Er-Src	breast:	n/a	chr3:50188359-50188371 chr3:50188476-50188488
29	GATA3	chr3:50187870-50189480	MCF-7	breast:	n/a	n/a
30	EP300	chr3:50188080-50188868	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:50188291-50188358	MCF-7	breast:	n/a	n/a
32	EP300	chr3:50188068-50188678	MCF-7	breast:	n/a	n/a
33	ELF1	chr3:50188107-50188735	MCF-7	breast:	n/a	n/a
34	GATA3	chr3:50188039-50188871	MCF-7	breast:	n/a	n/a
35	GATA3	chr3:50188077-50188684	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50157890..50164898-chr3:50186493..50191745,15	MCF-7	breast:
2	chr3:50187119..50189930-chr3:50262235..50264960,2	MCF-7	breast:
3	chr3:50187141..50189359-chr3:50306420..50308103,2	MCF-7	breast:
4	chr3:50187263..50189349-chr5:111741686..111743310,2	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000012171	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510755	0.95[GIH][hapmap]
rs1061474	0.89[JPT][hapmap]
rs1138536	0.89[JPT][hapmap]
rs12629572	0.85[GIH][hapmap]
rs12631337	0.93[ASN][1000 genomes]
rs1989839	0.85[GIH][hapmap]
rs2073498	0.90[GIH][hapmap]
rs2097247	0.81[AMR][1000 genomes]
rs2236939	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2301639	0.95[GIH][hapmap]
rs2526383	0.85[EUR][1000 genomes]
rs2526392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2526395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526400	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2624826	0.89[JPT][hapmap]
rs2624836	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624840	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2624842	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs28365992	0.90[GIH][hapmap]
rs2856237	0.89[JPT][hapmap]
rs2856238	0.89[JPT][hapmap]
rs2859580	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3806708	0.90[GIH][hapmap]
rs57319506	0.81[AMR][1000 genomes]
rs57462170	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57842657	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58051625	0.81[AMR][1000 genomes]
rs6446201	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446202	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6776145	0.85[GIH][hapmap]
rs739431	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap]
rs7642692	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831967	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
15	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
16	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
22	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
24	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2526396	SLC25A20	cis	cerebellum	SCAN
rs2526396	SFMBT1	cis	parietal	SCAN
rs2526396	DALRD3	cis	parietal	SCAN
rs2526396	NEK4	cis	parietal	SCAN
rs2526396	ARIH2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50177200-50191800	Weak transcription	Right Ventricle	heart
2	chr3:50177600-50191000	Weak transcription	Lung	lung
3	chr3:50183600-50192000	Enhancers	Esophagus	oesophagus
4	chr3:50183800-50189800	Enhancers	Fetal Stomach	stomach
5	chr3:50185000-50189600	Enhancers	Fetal Lung	lung
6	chr3:50186200-50188400	Weak transcription	Fetal Brain Male	brain
7	chr3:50186200-50191600	Weak transcription	Fetal Brain Female	brain
8	chr3:50187200-50188400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:50187200-50188400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:50187200-50188800	Flanking Active TSS	HepG2	liver
11	chr3:50187200-50189600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:50187200-50189800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:50187200-50190000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:50187400-50188400	Enhancers	Spleen	Spleen
15	chr3:50187400-50188800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:50187400-50188800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:50187400-50188800	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:50187400-50189000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr3:50187400-50189200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:50187400-50189400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:50187400-50189400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:50187400-50189400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:50187400-50189400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:50187400-50189600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:50187400-50189800	Enhancers	Placenta	Placenta
26	chr3:50187400-50190000	Enhancers	Fetal Muscle Leg	muscle
27	chr3:50187400-50190000	Enhancers	Fetal Thymus	thymus
28	chr3:50187600-50188400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:50187600-50188400	Enhancers	Fetal Kidney	kidney
30	chr3:50187600-50188600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:50187600-50188600	Enhancers	NHEK	skin
32	chr3:50187600-50189200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr3:50187600-50189400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr3:50187600-50189600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:50187600-50191800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:50187600-50192000	Enhancers	HMEC	breast
37	chr3:50187600-50192400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:50187800-50189800	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:50187800-50189800	Enhancers	Gastric	stomach
40	chr3:50187800-50190000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr3:50188000-50189400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr3:50188200-50188400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:50188200-50188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:50188200-50189200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:50188200-50189400	Enhancers	Fetal Intestine Small	intestine
46	chr3:50188200-50189600	Enhancers	H1 Cell Line	embryonic stem cell

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