Variant report

Variant	rs6785502
Chromosome Location	chr3:158542809-158542810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158542269..158544123-chr3:158547510..158549847,2	K562	blood:
2	chr3:158537210..158539822-chr3:158541591..158543597,3	K562	blood:
3	chr3:158541719..158543947-chr3:158545582..158547779,3	K562	blood:
4	chr3:158538165..158539695-chr3:158541319..158543916,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118855	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1604644	0.82[ASN][1000 genomes]
rs2364910	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35388278	0.88[ASN][1000 genomes]
rs3765083	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs4680470	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs6778714	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.88[ASN][1000 genomes]
rs6807246	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs751834	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs905457	0.86[ASN][1000 genomes]
rs9290029	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9839548	0.80[ASN][1000 genomes]
rs9846998	0.81[ASN][1000 genomes]
rs9855921	0.81[ASW][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs9877166	0.88[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	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6785502	MFSD1	cis	cerebellum	SCAN
rs6785502	SCHIP1	cis	lymphoblastoid	seeQTL
rs6785502	GFM1	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
2	chr3:158520600-158543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:158520800-158545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:158521000-158543200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:158521400-158544400	Weak transcription	HepG2	liver
6	chr3:158522400-158550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:158523000-158544000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:158527800-158543200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:158527800-158554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:158528000-158547000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:158528000-158549400	Weak transcription	Dnd41	blood
12	chr3:158528600-158549600	Weak transcription	Fetal Kidney	kidney
13	chr3:158528800-158547200	Weak transcription	Psoas Muscle	Psoas
14	chr3:158529400-158544800	Weak transcription	Hela-S3	cervix
15	chr3:158529600-158544200	Weak transcription	Fetal Heart	heart
16	chr3:158530400-158543800	Weak transcription	Fetal Brain Male	brain
17	chr3:158532200-158551800	Weak transcription	NHEK	skin
18	chr3:158532400-158557800	Weak transcription	Gastric	stomach
19	chr3:158533000-158543000	Weak transcription	Fetal Intestine Small	intestine
20	chr3:158533000-158543000	Weak transcription	Fetal Stomach	stomach
21	chr3:158533000-158548000	Weak transcription	Pancreas	Pancrea
22	chr3:158533000-158551000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:158533000-158556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:158533000-158559600	Weak transcription	Right Ventricle	heart
25	chr3:158533200-158544600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:158533200-158547600	Weak transcription	A549	lung
27	chr3:158534400-158550800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:158535400-158550600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:158535400-158551200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:158535400-158551200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:158535600-158543400	Strong transcription	Primary B cells from cord blood	blood
32	chr3:158535600-158543600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr3:158535600-158543600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:158535600-158543600	Strong transcription	Fetal Thymus	thymus
35	chr3:158535600-158544000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:158535600-158545600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:158535600-158545600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:158535600-158545600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:158535600-158546200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:158535600-158546200	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:158535600-158546400	Strong transcription	Osteobl	bone
42	chr3:158535600-158548200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:158535600-158548600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:158535600-158550200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:158535600-158550200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:158535600-158550600	Strong transcription	Liver	Liver
47	chr3:158535600-158550800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:158535800-158544000	Strong transcription	Primary T cells from cord blood	blood
49	chr3:158535800-158544200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr3:158535800-158545800	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links