Variant report

Variant	rs2526393
Chromosome Location	chr3:50189173-50189174
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50188591-50189259	MCF-7	breast:	n/a	n/a
2	NR2F2	chr3:50187971-50189510	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:50188332-50189484	MCF-7	breast:	n/a	n/a
4	CHD2	chr3:50188974-50189208	HepG2	liver:	n/a	n/a
5	ZNF217	chr3:50188018-50189463	MCF-7	breast:	n/a	n/a
6	GATA3	chr3:50187870-50189480	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50157890..50164898-chr3:50186493..50191745,15	MCF-7	breast:
2	chr3:50188380..50190870-chr3:50242074..50244308,2	K562	blood:
3	chr3:50187119..50189930-chr3:50262235..50264960,2	MCF-7	breast:
4	chr3:50188876..50190938-chr3:50352626..50354846,2	MCF-7	breast:
5	chr3:50187141..50189359-chr3:50306420..50308103,2	MCF-7	breast:
6	chr3:50188360..50189915-chr3:50190930..50193698,2	K562	blood:
7	chr3:50187263..50189349-chr5:111741686..111743310,2	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000188338	Chromatin interaction
ENSG00000235016	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1061474	0.89[JPT][hapmap]
rs1138536	0.89[JPT][hapmap]
rs12631337	0.93[ASN][1000 genomes]
rs2236939	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526383	0.85[EUR][1000 genomes]
rs2526392	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[JPT][hapmap];0.95[YRI][hapmap]
rs2526395	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]
rs2526396	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]
rs2526400	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2624826	0.89[JPT][hapmap]
rs2624836	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624840	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2624842	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2856237	0.89[JPT][hapmap]
rs2856238	0.89[JPT][hapmap]
rs2859580	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57462170	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57842657	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446201	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446202	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs739431	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs7642692	1.00[CEU][hapmap];0.83[CHB][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

No data

Chromatin state (count:50 , 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	chr3:50186200-50191600	Weak transcription	Fetal Brain Female	brain
7	chr3:50187200-50189600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:50187200-50189800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:50187200-50190000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:50187400-50189200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:50187400-50189400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:50187400-50189400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:50187400-50189400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:50187400-50189400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:50187400-50189600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:50187400-50189800	Enhancers	Placenta	Placenta
17	chr3:50187400-50190000	Enhancers	Fetal Muscle Leg	muscle
18	chr3:50187400-50190000	Enhancers	Fetal Thymus	thymus
19	chr3:50187600-50189200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:50187600-50189400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr3:50187600-50189600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:50187600-50191800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:50187600-50192000	Enhancers	HMEC	breast
24	chr3:50187600-50192400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:50187800-50189800	Enhancers	Duodenum Mucosa	Duodenum
26	chr3:50187800-50189800	Enhancers	Gastric	stomach
27	chr3:50187800-50190000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:50188000-50189400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr3:50188200-50189200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:50188200-50189400	Enhancers	Fetal Intestine Small	intestine
31	chr3:50188200-50189600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr3:50188400-50189200	Enhancers	Fetal Brain Male	brain
33	chr3:50188400-50189200	Weak transcription	Fetal Kidney	kidney
34	chr3:50188400-50189600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:50188600-50189200	Enhancers	Liver	Liver
36	chr3:50188600-50189200	Enhancers	Colonic Mucosa	Colon
37	chr3:50188600-50189400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:50188600-50189400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr3:50188600-50189400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:50188600-50189400	Flanking Active TSS	NHEK	skin
41	chr3:50188800-50189200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:50188800-50189200	Enhancers	Stomach Mucosa	stomach
43	chr3:50188800-50189600	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr3:50188800-50189800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr3:50188800-50190000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:50188800-50191800	Enhancers	Spleen	Spleen
47	chr3:50189000-50189200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:50189000-50189200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:50189000-50189200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:50189000-50190000	Enhancers	Skeletal Muscle Male	skeletal muscle

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