Variant report

Variant	rs6973579
Chromosome Location	chr7:8168466-8168467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8167235..8170008-chr7:8174877..8177246,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10156091	1.00[CHB][hapmap]
rs10215221	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058522	0.91[ASN][1000 genomes]
rs2058523	0.91[ASN][1000 genomes]
rs2192346	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34500452	0.85[ASN][1000 genomes]
rs3807845	0.85[ASN][1000 genomes]
rs59897701	0.85[ASN][1000 genomes]
rs6463769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945305	0.91[ASN][1000 genomes]
rs7794722	0.85[ASN][1000 genomes]
rs7795490	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1020686	chr7:8095118-8311985	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv538723	chr7:8095118-8311985	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6973579	ICA1	cis	cerebellum	SCAN
rs6973579	COL28A1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8150600-8200000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:8151400-8173800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:8152600-8183200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:8153800-8169800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:8155800-8185600	Weak transcription	Fetal Heart	heart
6	chr7:8159000-8169000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:8159200-8186600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:8160600-8168600	Weak transcription	K562	blood
9	chr7:8162000-8177400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:8162400-8192800	Weak transcription	Colonic Mucosa	Colon
11	chr7:8162600-8168800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:8162800-8171600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:8163400-8171400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr7:8164000-8168600	Enhancers	Fetal Thymus	thymus
15	chr7:8164000-8171400	Enhancers	Primary T cells from cord blood	blood
16	chr7:8164600-8169400	Enhancers	Primary B cells from peripheral blood	blood
17	chr7:8165400-8171400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr7:8165400-8172800	Weak transcription	Small Intestine	intestine
19	chr7:8165600-8171600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:8165800-8170600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:8166000-8168800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:8166000-8168800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr7:8166000-8169400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr7:8166000-8171200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:8166000-8172400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr7:8166000-8173600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:8166000-8179600	Weak transcription	Right Ventricle	heart
28	chr7:8166000-8179800	Weak transcription	Gastric	stomach
29	chr7:8166000-8180200	Weak transcription	Fetal Intestine Large	intestine
30	chr7:8166000-8180200	Weak transcription	Spleen	Spleen
31	chr7:8166000-8186600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:8166200-8170400	Weak transcription	Brain Anterior Caudate	brain
33	chr7:8166400-8168800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:8166400-8170600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr7:8166400-8171200	Weak transcription	Primary B cells from cord blood	blood
36	chr7:8166800-8168600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:8167200-8170600	Weak transcription	Thymus	Thymus
38	chr7:8167600-8168600	Enhancers	Esophagus	oesophagus
39	chr7:8167600-8169200	Flanking Active TSS	GM12878-XiMat	blood
40	chr7:8167800-8168600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:8167800-8168600	Flanking Active TSS	Ovary	ovary
42	chr7:8167800-8169800	Weak transcription	Fetal Intestine Small	intestine
43	chr7:8167800-8179800	Weak transcription	Lung	lung
44	chr7:8167800-8192200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:8168000-8168600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:8168000-8168800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr7:8168000-8169200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:8168000-8173200	Weak transcription	Adipose Nuclei	Adipose
49	chr7:8168000-8183200	Weak transcription	Left Ventricle	heart
50	chr7:8168200-8169200	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links