Variant report

Variant	rs6975531
Chromosome Location	chr7:38219350-38219351
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38218320..38221053-chr7:38246020..38247686,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1019180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10226230	0.80[GIH][hapmap];0.84[MEX][hapmap]
rs10233340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10240479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10282407	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10480164	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12531618	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17171307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860522	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2159499	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35997004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723733	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723738	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55864286	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6462817	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462818	0.81[AFR][1000 genomes]
rs7784752	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7788819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7795499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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
3	esv2762664	chr7:38201814-38228480	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription 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	37 gene(s)	inside rSNPs	diseases
5	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv830964	chr7:38218708-38390518	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6975531	STARD3NL	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38217000-38219400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr7:38217000-38219400	Active TSS	GM12878-XiMat	blood
3	chr7:38217000-38219600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr7:38217000-38219800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr7:38217200-38219400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:38217200-38219400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:38217200-38219400	Active TSS	Ovary	ovary
8	chr7:38217200-38219600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:38217200-38219600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:38217200-38220000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr7:38217200-38220000	Active TSS	Stomach Smooth Muscle	stomach
12	chr7:38217200-38220600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr7:38218200-38219600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr7:38218400-38219400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr7:38218400-38219400	Weak transcription	Spleen	Spleen
16	chr7:38218400-38219600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:38218400-38219800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr7:38218400-38220000	Flanking Active TSS	Dnd41	blood
19	chr7:38218400-38220200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:38218400-38220800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:38218400-38223400	Weak transcription	Small Intestine	intestine
22	chr7:38218400-38225000	Weak transcription	Gastric	stomach
23	chr7:38218600-38219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:38218600-38219400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:38218600-38219400	Weak transcription	Left Ventricle	heart
26	chr7:38218600-38219400	Weak transcription	Lung	lung
27	chr7:38218600-38219400	Weak transcription	Pancreas	Pancrea
28	chr7:38218600-38219600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr7:38218600-38219600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr7:38218600-38219600	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr7:38218600-38219600	Flanking Active TSS	Fetal Brain Male	brain
32	chr7:38218600-38219600	Flanking Active TSS	Fetal Heart	heart
33	chr7:38218600-38219600	Flanking Active TSS	NHEK	skin
34	chr7:38218600-38219800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr7:38218600-38219800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr7:38218600-38220000	Flanking Active TSS	HMEC	breast
37	chr7:38218600-38220200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:38218600-38220200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:38218600-38220600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr7:38218600-38221000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr7:38218600-38221200	Flanking Active TSS	HUVEC	blood vessel
42	chr7:38218600-38221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:38218600-38222400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:38218600-38224000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr7:38218600-38226200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:38218600-38226600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:38218600-38259200	Weak transcription	Colonic Mucosa	Colon
48	chr7:38218800-38219400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr7:38218800-38219400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:38218800-38219400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links