Variant report

Variant	rs4946768
Chromosome Location	chr6:107027481-107027482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:107026128..107027753-chr6:107075695..107078557,2	K562	blood:

Variant related genes	Relation type
ENSG00000130347	Chromatin interaction
ENSG00000130348	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1026622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759221	0.96[EUR][1000 genomes]
rs11968064	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs12210786	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12214557	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526141	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17052215	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2883075	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945758	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945759	0.83[MKK][hapmap]
rs4946762	0.80[MKK][hapmap]
rs4946764	0.94[ASW][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4946774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57424436	0.99[EUR][1000 genomes]
rs58972320	0.99[EUR][1000 genomes]
rs6911512	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935354	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6940963	0.91[AFR][1000 genomes]
rs7738230	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7751749	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9384622	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9384623	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9384624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386567	0.83[AFR][1000 genomes]
rs9386571	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386574	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400031	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480692	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965347	1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4946768	QRSL1	cis	parietal	SCAN
rs4946768	QRSL1	cis	cerebellum	SCAN
rs4946768	SCML4	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
2	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
4	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:107008400-107027600	Strong transcription	Primary T cells from cord blood	blood
6	chr6:107010200-107064600	Weak transcription	A549	lung
7	chr6:107011800-107030000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:107012800-107030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:107014400-107038800	Weak transcription	Fetal Brain Female	brain
10	chr6:107016200-107039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:107017000-107032800	Weak transcription	K562	blood
12	chr6:107017800-107041000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:107018000-107030800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:107018000-107052600	Weak transcription	Colonic Mucosa	Colon
15	chr6:107018400-107066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:107018400-107076400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:107018600-107029600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:107018600-107030000	Weak transcription	Fetal Intestine Large	intestine
19	chr6:107018600-107039000	Weak transcription	Placenta	Placenta
20	chr6:107018800-107030200	Weak transcription	Dnd41	blood
21	chr6:107018800-107039400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:107018800-107076200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:107019000-107029200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:107019000-107029400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:107019000-107029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:107019000-107030200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:107019000-107030200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:107019000-107076200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:107019200-107029400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:107019200-107034800	Weak transcription	GM12878-XiMat	blood
31	chr6:107019400-107034400	Weak transcription	NHEK	skin
32	chr6:107019400-107035200	Weak transcription	Fetal Lung	lung
33	chr6:107019600-107029200	Weak transcription	Fetal Thymus	thymus
34	chr6:107019600-107029400	Weak transcription	Spleen	Spleen
35	chr6:107019800-107029000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:107019800-107076400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:107020200-107037600	Weak transcription	Fetal Heart	heart
38	chr6:107020600-107029200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:107020600-107030600	Weak transcription	Thymus	Thymus
40	chr6:107020600-107032200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr6:107020800-107030000	Weak transcription	Esophagus	oesophagus
42	chr6:107021000-107029200	Weak transcription	Pancreas	Pancrea
43	chr6:107021600-107033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:107022000-107076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:107022600-107027800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr6:107023000-107030800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:107023200-107030200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:107023200-107038200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:107023200-107038600	Weak transcription	Brain Germinal Matrix	brain
50	chr6:107023400-107029200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links