Variant report

Variant	rs6446203
Chromosome Location	chr3:50377129-50377130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50376934-50379464	HL-60	blood:	n/a	n/a
2	POLR2A	chr3:50376960-50378970	HL-60	blood:	n/a	n/a
3	POLR2A	chr3:50377107-50378957	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:50377067-50379419	NB4	blood:	n/a	n/a
5	POLR2A	chr3:50377102-50379641	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:50377116-50377295	K562	blood:	n/a	n/a
7	POLR2A	chr3:50377051-50378932	GM12878	blood:	n/a	n/a
8	TBP	chr3:50377117-50377211	K562	blood:	n/a	n/a
9	EGR1	chr3:50376882-50377211	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:50376891..50380040-chr3:50387225..50390511,3	MCF-7	breast:
2	chr3:50325622..50330493-chr3:50373581..50377874,6	K562	blood:
3	chr3:50356822..50362778-chr3:50372728..50378128,10	MCF-7	breast:
4	chr3:50375263..50377501-chr3:50606436..50608027,2	K562	blood:
5	chr3:50371739..50377775-chr3:50378206..50384768,10	MCF-7	breast:
6	chr3:50264037..50266762-chr3:50376102..50379754,3	K562	blood:
7	chr3:50376122..50377896-chr3:50582869..50585002,2	K562	blood:

No data

Variant related genes	Relation type
RASSF1	TF binding region
ZMYND10-AS1	TF binding region
ENSG00000235058	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000114395	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000068001	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000272104	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1034408	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs1034409	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs1107312	1.00[CEU][hapmap]
rs11914549	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916258	1.00[GIH][hapmap]
rs11928538	1.00[GIH][hapmap]
rs1894324	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2157328	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs2187815	1.00[CEU][hapmap]
rs2236944	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs2236969	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs2236972	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs2236977	1.00[CEU][hapmap]
rs2236978	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs2236982	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs2236990	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs2282757	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs2298953	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs2298954	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs35742391	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3774753	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs3806706	1.00[CEU][hapmap]
rs41305886	0.84[AFR][1000 genomes]
rs4422301	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs55876418	0.87[AFR][1000 genomes]
rs56287038	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57405128	0.87[AFR][1000 genomes]
rs57453427	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58415636	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59790001	0.85[AFR][1000 genomes]
rs61382127	1.00[EUR][1000 genomes]
rs6767505	1.00[CEU][hapmap]
rs6768830	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6770258	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs6770669	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs73833373	0.85[AFR][1000 genomes]
rs743754	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs743755	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs743859	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs7610830	0.87[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7617345	0.90[AFR][1000 genomes]
rs7626470	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs7629917	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7634307	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs7636862	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7641224	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs7642779	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs7647409	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs7649603	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs886075	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9814606	0.88[YRI][hapmap]
rs9814874	1.00[CEU][hapmap]
rs9817768	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs9828829	1.00[CEU][hapmap]
rs9830408	1.00[CEU][hapmap]
rs9837658	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs9851719	0.82[EUR][1000 genomes]
rs9854585	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs9863307	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs9875873	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs9878345	0.82[EUR][1000 genomes]
rs9883222	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs9883635	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs9990256	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer 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	93 gene(s)	inside rSNPs	diseases
13	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	82 gene(s)	inside rSNPs	diseases
15	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
17	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
18	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
19	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
20	nsv590258	chr3:50368278-50381022	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50373800-50379200	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr3:50374200-50379000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:50375000-50379600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:50375200-50378000	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr3:50375200-50379000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr3:50375200-50379000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr3:50375200-50379200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr3:50375200-50379200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr3:50375400-50377800	Enhancers	Fetal Heart	heart
10	chr3:50375400-50377800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:50375400-50378000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:50375400-50379400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr3:50375600-50377200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:50375600-50377200	Weak transcription	Ovary	ovary
15	chr3:50375600-50377200	Enhancers	Spleen	Spleen
16	chr3:50375600-50377400	Weak transcription	Gastric	stomach
17	chr3:50375600-50377400	Weak transcription	Left Ventricle	heart
18	chr3:50375600-50377600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:50375600-50377800	Weak transcription	Aorta	Aorta
20	chr3:50375800-50377200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:50375800-50377200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:50375800-50377200	Enhancers	Colon Smooth Muscle	Colon
23	chr3:50375800-50377200	Enhancers	Stomach Mucosa	stomach
24	chr3:50375800-50377200	Weak transcription	HUVEC	blood vessel
25	chr3:50375800-50377200	Enhancers	NHEK	skin
26	chr3:50375800-50377400	Weak transcription	Brain Angular Gyrus	brain
27	chr3:50375800-50377600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:50375800-50377600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:50375800-50377600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:50375800-50377800	Enhancers	Lung	lung
31	chr3:50375800-50377800	Weak transcription	Psoas Muscle	Psoas
32	chr3:50375800-50378000	Weak transcription	HMEC	breast
33	chr3:50375800-50378000	Enhancers	HSMMtube	muscle
34	chr3:50376000-50380200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:50376200-50377200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:50376400-50377200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:50376400-50377200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:50376400-50377200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:50376400-50377200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:50376400-50377200	Weak transcription	HSMM	muscle
41	chr3:50376400-50377400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:50376400-50377400	Weak transcription	Esophagus	oesophagus
43	chr3:50376400-50377400	Weak transcription	Right Atrium	heart
44	chr3:50376400-50377400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:50376400-50377400	Enhancers	Thymus	Thymus
46	chr3:50376400-50377600	Weak transcription	Brain Substantia Nigra	brain
47	chr3:50376400-50377800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:50376400-50378000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:50376400-50378600	Active TSS	Placenta	Placenta
50	chr3:50376600-50377200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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