Variant report

Variant	rs6446202
Chromosome Location	chr3:50219991-50219992
allele	C/G
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	POLR2A	chr3:50219972-50220142	Hela-S3	cervix:	n/a	n/a
2	MAX	chr3:50219750-50220203	K562	blood:	n/a	n/a
3	POLR2A	chr3:50219943-50220037	HUVEC	blood vessel:	n/a	n/a
4	GATA2	chr3:50219331-50220135	SH-SY5Y	brain:	n/a	chr3:50219628-50219638 chr3:50219959-50219975 chr3:50219963-50219970 chr3:50219963-50219970 chr3:50219962-50219972 chr3:50219628-50219635 chr3:50219963-50219970 chr3:50219617-50219634 chr3:50219626-50219635 chr3:50219626-50219636
5	POLR2A	chr3:50219991-50220128	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:50219737-50220140	HepG2	liver:	n/a	n/a
7	EP300	chr3:50219255-50220007	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50218401..50220545-chr3:50229488..50231128,2	MCF-7	breast:
2	chr3:50144744..50147316-chr3:50219770..50222620,2	K562	blood:
3	chr3:50192650..50196663-chr3:50219720..50222472,4	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000001617	Chromatin interaction
ENSG00000235016	Chromatin interaction
ENSG00000114349	Chromatin interaction
ENSG00000003756	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs12631337	0.80[ASN][1000 genomes]
rs13060128	0.82[JPT][hapmap]
rs2013208	0.82[JPT][hapmap]
rs2071802	0.81[CEU][hapmap]
rs2236939	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2240326	0.82[JPT][hapmap]
rs2240327	0.82[JPT][hapmap]
rs2240329	0.82[JPT][hapmap]
rs2301166	0.90[JPT][hapmap]
rs2353579	0.82[JPT][hapmap]
rs2526392	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526393	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526394	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs2526395	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526396	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526400	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526748	0.82[JPT][hapmap]
rs2526751	0.82[JPT][hapmap]
rs2526754	0.82[JPT][hapmap]
rs2624836	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624837	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624840	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624842	0.85[CEU][hapmap];0.85[ASN][1000 genomes]
rs2624847	0.82[JPT][hapmap]
rs2624853	0.82[JPT][hapmap]
rs2856234	0.90[JPT][hapmap]
rs2859580	0.85[EUR][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs4688689	0.82[JPT][hapmap]
rs4688690	0.82[JPT][hapmap]
rs4688755	0.82[JPT][hapmap]
rs4688758	0.82[JPT][hapmap]
rs57462170	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57842657	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446193	0.82[JPT][hapmap]
rs6446201	0.84[ASN][1000 genomes]
rs6765484	0.82[JPT][hapmap]
rs739431	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7621352	0.82[JPT][hapmap]
rs7628058	0.82[JPT][hapmap]
rs7642692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311446	0.82[JPT][hapmap]
rs9814664	0.82[JPT][hapmap]
rs9831967	0.87[ASN][1000 genomes]
rs9861216	0.82[JPT][hapmap]
rs9866695	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 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
25	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer 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
26	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
28	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50204600-50226600	Weak transcription	Brain Anterior Caudate	brain
2	chr3:50205400-50226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:50205400-50226600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:50206400-50226600	Weak transcription	NHLF	lung
5	chr3:50208800-50226600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:50208800-50226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:50208800-50226600	Weak transcription	Osteobl	bone
8	chr3:50210400-50229200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:50210400-50242400	Weak transcription	Right Atrium	heart
10	chr3:50210600-50225000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:50210600-50229400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:50211400-50230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:50212200-50226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:50213600-50222400	Weak transcription	Fetal Kidney	kidney
15	chr3:50213600-50226400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:50214200-50230600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:50215000-50220200	Weak transcription	Colonic Mucosa	Colon
18	chr3:50215000-50220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:50215000-50222000	Weak transcription	Aorta	Aorta
20	chr3:50215000-50223000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:50215000-50226600	Weak transcription	HSMMtube	muscle
22	chr3:50216600-50226200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:50217000-50226000	Strong transcription	NHEK	skin
24	chr3:50217600-50221400	Weak transcription	Liver	Liver
25	chr3:50217800-50221000	Weak transcription	HepG2	liver
26	chr3:50218000-50222200	Enhancers	Placenta	Placenta
27	chr3:50218000-50225600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:50218000-50226200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:50218000-50226200	Weak transcription	Stomach Mucosa	stomach
30	chr3:50218000-50228600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:50218800-50226200	Strong transcription	Brain Germinal Matrix	brain
32	chr3:50219000-50225800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr3:50219200-50220000	Enhancers	K562	blood
34	chr3:50219200-50226000	Strong transcription	Fetal Brain Female	brain
35	chr3:50219200-50226200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:50219200-50226400	Strong transcription	Fetal Stomach	stomach
37	chr3:50219400-50220200	Strong transcription	HUVEC	blood vessel
38	chr3:50219400-50220400	Genic enhancers	Hela-S3	cervix
39	chr3:50219400-50220600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:50219400-50223200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:50219400-50224000	Strong transcription	Right Ventricle	heart
42	chr3:50219400-50224600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:50219400-50225400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:50219400-50225400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:50219400-50226000	Strong transcription	Lung	lung
46	chr3:50219400-50226200	Strong transcription	Adipose Nuclei	Adipose
47	chr3:50219400-50226600	Strong transcription	HMEC	breast
48	chr3:50219600-50220000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:50219600-50220200	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr3:50219600-50220400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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