Variant report

Variant	rs9863901
Chromosome Location	chr3:194996737-194996738
allele	A/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	chr3:194993689-194996866	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194990271..194992764-chr3:194994105..194997544,4	K562	blood:

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10933706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11718218	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927933	0.80[ASN][1000 genomes]
rs13062574	0.93[ASN][1000 genomes]
rs1832667	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050810	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410803	0.89[EUR][1000 genomes]
rs2410839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410840	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28375276	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688106	0.86[ASN][1000 genomes]
rs2898570	0.87[EUR][1000 genomes]
rs3087885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677820	0.93[ASN][1000 genomes]
rs4677825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677830	0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58204696	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437467	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780743	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781643	0.92[EUR][1000 genomes]
rs6791601	0.92[EUR][1000 genomes]
rs6791943	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs6795263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73080837	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73080839	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610022	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612694	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638924	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7640100	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643947	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7644002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649142	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823299	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823304	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823309	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823312	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823313	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823533	0.80[ASN][1000 genomes]
rs823534	0.80[ASN][1000 genomes]
rs862066	0.80[ASN][1000 genomes]
rs9288747	0.86[ASN][1000 genomes]
rs9831944	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832920	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9870813	1.00[JPT][hapmap]
rs9878312	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992400-195009000	Weak transcription	Spleen	Spleen
2	chr3:194992600-195003600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:194992600-195003600	Weak transcription	Small Intestine	intestine
4	chr3:194992600-195008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:194992600-195008800	Weak transcription	Lung	lung
6	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
7	chr3:194992800-194997200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:194992800-195003600	Weak transcription	Esophagus	oesophagus
9	chr3:194992800-195003600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:194992800-195003600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:194992800-195003600	Weak transcription	Left Ventricle	heart
12	chr3:194992800-195003600	Weak transcription	Psoas Muscle	Psoas
13	chr3:194992800-195003600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:194992800-195004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:194992800-195005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:194992800-195008600	Weak transcription	Ovary	ovary
17	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
18	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
19	chr3:194993000-194996800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:194993000-194997400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:194993000-194997400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:194993000-194997400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:194993000-194997400	Weak transcription	NH-A	brain
24	chr3:194993000-194997800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:194993000-194997800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:194993000-194998000	Weak transcription	Fetal Lung	lung
27	chr3:194993000-194998400	Weak transcription	Thymus	Thymus
28	chr3:194993000-194998600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:194993000-194998800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:194993000-194999200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:194993000-194999200	Weak transcription	Placenta	Placenta
32	chr3:194993000-194999400	Weak transcription	Primary T cells from cord blood	blood
33	chr3:194993000-194999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:194993000-194999400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:194993000-195001200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:194993000-195003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:194993000-195003400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:194993000-195003400	Weak transcription	Adipose Nuclei	Adipose
39	chr3:194993000-195003600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:194993000-195003600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:194993000-195003600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:194993000-195003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:194993000-195003600	Weak transcription	Fetal Intestine Small	intestine
44	chr3:194993000-195003600	Weak transcription	Fetal Stomach	stomach
45	chr3:194993000-195003600	Weak transcription	Gastric	stomach
46	chr3:194993000-195003600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:194993000-195003600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:194993000-195003600	Weak transcription	Stomach Mucosa	stomach
49	chr3:194993000-195003800	Weak transcription	Fetal Brain Female	brain
50	chr3:194993000-195003800	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links