Variant report

Variant	rs879606
Chromosome Location	chr17:37781849-37781850
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	CTCF	chr17:37781700-37781850	GM12870	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37781012..37783798-chr17:37885303..37888164,4	K562	blood:
2	chr17:37777756..37783081-chr17:37819129..37825010,9	K562	blood:
3	chr17:37780595..37782911-chr17:37786267..37787886,2	MCF-7	breast:
4	chr17:37778202..37782049-chr17:37783082..37786622,6	K562	blood:

Variant related genes	Relation type
PPP1R1B	TF binding region
ENSG00000173991	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000131771	Chromatin interaction
ENSG00000141741	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1018246	0.87[ASN][1000 genomes]
rs1053651	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs10852934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651497	0.99[ASN][1000 genomes]
rs11657058	0.83[CEU][hapmap]
rs11657153	0.83[CEU][hapmap]
rs11658786	0.89[ASN][1000 genomes]
rs11869286	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12150047	0.83[CEU][hapmap]
rs12150298	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12150603	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12453682	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12937013	0.83[CEU][hapmap]
rs12938099	0.83[CEU][hapmap]
rs12940986	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12947506	0.83[CEU][hapmap]
rs14050	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1476278	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1495099	0.99[ASN][1000 genomes]
rs1495100	0.87[ASN][1000 genomes]
rs1495101	0.87[ASN][1000 genomes]
rs1495102	0.87[ASN][1000 genomes]
rs1565920	0.87[ASN][1000 genomes]
rs1565922	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1874228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1877031	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2247862	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2271308	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2271309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2313171	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2517952	0.80[ASN][1000 genomes]
rs2517953	0.82[ASN][1000 genomes]
rs2517954	0.81[ASN][1000 genomes]
rs2517955	0.80[ASN][1000 genomes]
rs2517956	0.80[ASN][1000 genomes]
rs2517957	0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2517958	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2517959	0.81[ASN][1000 genomes]
rs2934951	0.87[ASN][1000 genomes]
rs2934952	0.87[ASN][1000 genomes]
rs2934953	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2934956	0.87[ASN][1000 genomes]
rs2941503	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2941504	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2941505	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2941506	0.87[ASN][1000 genomes]
rs2952151	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2952152	0.86[ASN][1000 genomes]
rs33953566	1.00[ASN][1000 genomes]
rs3751903	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764352	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3764353	0.99[ASN][1000 genomes]
rs3794712	0.95[ASN][1000 genomes]
rs3817160	0.99[ASN][1000 genomes]
rs407307	0.84[ASN][1000 genomes]
rs4794817	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795379	0.83[CEU][hapmap]
rs4795388	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4795389	0.99[ASN][1000 genomes]
rs4795390	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732083	0.87[ASN][1000 genomes]
rs732084	0.87[ASN][1000 genomes]
rs7503377	0.83[CEU][hapmap]
rs8069074	0.83[CEU][hapmap]
rs8077172	0.87[ASN][1000 genomes]
rs8078228	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs881844	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs903501	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs903502	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs907087	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs907088	0.87[ASN][1000 genomes]
rs907089	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs907090	0.87[ASN][1000 genomes]
rs907094	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9303274	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs931992	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs9646419	0.83[CEU][hapmap]
rs9675194	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9915323	0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs9972882	0.89[ASW][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS 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	53 gene(s)	inside rSNPs	diseases
5	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv908208	chr17:37749259-37781849	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv908209	chr17:37749259-37790340	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv908210	chr17:37761202-37781849	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv908211	chr17:37765047-37782410	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv908212	chr17:37765047-37790340	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
18	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs879606	SLFN14	cis	parietal	SCAN
rs879606	IGFBP4	cis	parietal	SCAN
rs879606	NEUROD2	cis	cerebellum	SCAN
rs879606	SPACA3	cis	parietal	SCAN
rs879606	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs879606	SLFN12	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37775000-37782400	Weak transcription	Gastric	stomach
2	chr17:37775200-37782600	Weak transcription	Lung	lung
3	chr17:37775200-37782800	Weak transcription	Right Atrium	heart
4	chr17:37775400-37782800	Weak transcription	Right Ventricle	heart
5	chr17:37778400-37782600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:37778800-37782400	Enhancers	A549	lung
7	chr17:37778800-37790600	Weak transcription	K562	blood
8	chr17:37779200-37782200	Enhancers	Fetal Lung	lung
9	chr17:37779600-37782600	Weak transcription	Fetal Heart	heart
10	chr17:37780200-37783000	Weak transcription	Ovary	ovary
11	chr17:37780400-37782400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:37780800-37783200	Enhancers	Esophagus	oesophagus
13	chr17:37781000-37782000	Enhancers	Brain Anterior Caudate	brain
14	chr17:37781000-37782400	Bivalent Enhancer	Colonic Mucosa	Colon
15	chr17:37781000-37782600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:37781200-37782400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:37781200-37782600	Weak transcription	Fetal Brain Male	brain
18	chr17:37781200-37782600	Bivalent Enhancer	Fetal Stomach	stomach
19	chr17:37781200-37783000	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr17:37781400-37782000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:37781400-37782200	Enhancers	Fetal Intestine Large	intestine
22	chr17:37781400-37782600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:37781400-37782600	Bivalent Enhancer	Fetal Intestine Small	intestine
24	chr17:37781400-37782600	Enhancers	Pancreas	Pancrea
25	chr17:37781400-37782600	Enhancers	HMEC	breast
26	chr17:37781400-37782800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr17:37781400-37783000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:37781600-37782000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
29	chr17:37781600-37782400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
30	chr17:37781600-37782600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr17:37781600-37782600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr17:37781600-37782600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:37781600-37782800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:37781600-37782800	Bivalent Enhancer	NHEK	skin
35	chr17:37781600-37783000	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr17:37781800-37782000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:37781800-37782000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr17:37781800-37782000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
39	chr17:37781800-37782000	Enhancers	Hela-S3	cervix
40	chr17:37781800-37782600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
41	chr17:37781800-37782600	Bivalent Enhancer	Brain Hippocampus Middle	brain
42	chr17:37781800-37783000	Bivalent Enhancer	Fetal Thymus	thymus
43	chr17:37781800-37783000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion

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