Variant report

Variant	rs3735169
Chromosome Location	chr7:150034378-150034379
allele	C/T
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:4)
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	chr7:150034306-150034560	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:150034356-150036317	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:150032631-150038069	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:150032104-150036320	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:150033840-150035236	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:150033956-150034593	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:150030237..150032471-chr7:150033409..150035397,2	MCF-7	breast:
2	chr7:150034163..150038835-chr7:150063325..150067223,6	MCF-7	breast:
3	chr7:150018389..150025798-chr7:150030734..150040389,17	MCF-7	breast:
4	chr7:150025919..150029003-chr7:150032964..150036156,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261305	TF binding region
ENSG00000127399	Chromatin interaction
ENSG00000188707	Chromatin interaction
ENSG00000106526	Chromatin interaction
ENSG00000214022	Chromatin interaction
ENSG00000196456	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10248490	0.84[JPT][hapmap]
rs10259796	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10282458	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1047207	0.94[EUR][1000 genomes]
rs1047575	0.94[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1047586	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1051760	0.94[CEU][hapmap]
rs1051764	0.94[CEU][hapmap]
rs1051823	0.89[CEU][hapmap]
rs10952249	0.83[EUR][1000 genomes]
rs10952250	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10952252	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1132261	0.89[CEU][hapmap]
rs11764936	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765644	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765692	0.89[EUR][1000 genomes]
rs11766288	0.87[EUR][1000 genomes]
rs11767726	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs11769348	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773351	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974980	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs11975886	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11983355	0.86[EUR][1000 genomes]
rs1464752	0.87[EUR][1000 genomes]
rs1464753	0.89[EUR][1000 genomes]
rs17173617	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs17173681	0.94[CEU][hapmap]
rs17173682	0.94[CEU][hapmap]
rs17837498	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1916932	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1962004	0.86[CEU][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1983440	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2098053	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108851	0.86[EUR][1000 genomes]
rs2108852	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2108853	0.86[EUR][1000 genomes]
rs2108854	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2159234	0.86[EUR][1000 genomes]
rs2159235	0.86[EUR][1000 genomes]
rs2159236	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2373751	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28432021	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28439010	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3088207	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34489187	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735167	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3735171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735172	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3735173	0.87[EUR][1000 genomes]
rs3735174	0.87[EUR][1000 genomes]
rs3735175	0.86[EUR][1000 genomes]
rs3757423	0.94[CEU][hapmap]
rs3757425	0.89[CEU][hapmap]
rs3800780	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800781	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4395803	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4554381	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55715989	0.83[EUR][1000 genomes]
rs55881542	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55974958	0.94[EUR][1000 genomes]
rs56019796	0.83[EUR][1000 genomes]
rs56190213	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56923535	0.83[EUR][1000 genomes]
rs56998970	0.83[EUR][1000 genomes]
rs57888387	0.90[EUR][1000 genomes]
rs59572505	0.83[EUR][1000 genomes]
rs60268791	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60283368	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60467296	0.83[EUR][1000 genomes]
rs61421252	0.94[EUR][1000 genomes]
rs6722	0.94[CEU][hapmap]
rs6946097	0.89[CEU][hapmap]
rs6964110	0.94[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73170169	0.90[EUR][1000 genomes]
rs73170174	0.86[EUR][1000 genomes]
rs73170185	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73170192	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7781827	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7788316	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7800196	0.94[CEU][hapmap]
rs7806429	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs883138	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv508490	chr7:150006068-150051241	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 target site	50 gene(s)	inside rSNPs	diseases
6	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
9	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv518774	chr7:150020295-150036664	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv889457	chr7:150020295-150104410	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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 target site	50 gene(s)	inside rSNPs	diseases
13	nsv889458	chr7:150020295-150115183	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
14	nsv521407	chr7:150020295-150118590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs3735169	RARRES2	cis	normal skin	skin_eQTL
rs3735169	ACTR3C	cis	Muscle Skeletal	GTEx
rs3735169	LRRC61	cis	multi-tissue	Pritchard
rs3735169	LRRC61	cis	Muscle Skeletal	GTEx
rs3735169	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs3735169	LRRC61	cis	Adipose Subcutaneous	GTEx
rs3735169	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs3735169	ZBED6CL	cis	Whole Blood	GTEx
rs3735169	RARRES2	cis	multi-tissue	Pritchard
rs3735169	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs3735169	C7orf29	cis	multi-tissue	Pritchard
rs3735169	LRRC61	cis	Thyroid	GTEx
rs3735169	LRRC61	cis	lung	GTEx
rs3735169	REPIN1	cis	Muscle Skeletal	GTEx
rs3735169	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs3735169	LRRC61	cis	Esophagus Mucosa	GTEx
rs3735169	LRRC61	cis	Nerve Tibial	GTEx
rs3735169	LRRC61	cis	Artery Tibial	GTEx
rs3735169	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs3735169	ZBED6CL	cis	lung	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150021400-150037000	Weak transcription	Brain Substantia Nigra	brain
2	chr7:150021800-150037200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:150022000-150036400	Weak transcription	Fetal Kidney	kidney
4	chr7:150022200-150037200	Weak transcription	Small Intestine	intestine
5	chr7:150022400-150035600	Weak transcription	Fetal Heart	heart
6	chr7:150022400-150037400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:150022600-150036800	Strong transcription	Fetal Brain Female	brain
8	chr7:150025200-150035200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:150025200-150037600	Strong transcription	Dnd41	blood
10	chr7:150025800-150036000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:150025800-150037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:150026000-150035600	Weak transcription	Fetal Brain Male	brain
13	chr7:150026400-150035200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:150026400-150036800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:150027400-150035400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:150027600-150035200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:150027800-150035800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:150028000-150036600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:150028200-150037000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:150028400-150036400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr7:150028400-150037200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:150028800-150036200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:150029000-150034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:150029000-150036200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:150029000-150036200	Weak transcription	GM12878-XiMat	blood
26	chr7:150029200-150036800	Weak transcription	Primary B cells from cord blood	blood
27	chr7:150029200-150037000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr7:150030200-150036000	Weak transcription	HepG2	liver
29	chr7:150031000-150036600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:150031400-150034400	Enhancers	Liver	Liver
31	chr7:150031400-150034800	Weak transcription	Hela-S3	cervix
32	chr7:150031400-150037400	Weak transcription	K562	blood
33	chr7:150032200-150035200	Enhancers	Colon Smooth Muscle	Colon
34	chr7:150032400-150034400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr7:150032600-150035600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:150032600-150036800	Enhancers	Colonic Mucosa	Colon
37	chr7:150032800-150035000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:150032800-150035000	Weak transcription	HSMM	muscle
39	chr7:150032800-150035400	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr7:150032800-150035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:150033000-150035600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:150033000-150035600	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:150033000-150036000	Strong transcription	Primary T cells from cord blood	blood
44	chr7:150033000-150036200	Strong transcription	Fetal Thymus	thymus
45	chr7:150033000-150036400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr7:150033000-150036600	Genic enhancers	H1 Cell Line	embryonic stem cell
47	chr7:150033000-150036600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:150033000-150037200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr7:150033200-150034800	Weak transcription	Brain Angular Gyrus	brain
50	chr7:150033200-150034800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links