Variant report

Variant	rs11265621
Chromosome Location	chr1:154442960-154442961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154440133..154443020-chr1:154529581..154531966,2	MCF-7	breast:
2	chr1:154429933..154432687-chr1:154440659..154442962,2	K562	blood:
3	chr1:154431187..154433172-chr1:154441462..154443845,2	K562	blood:

Variant related genes	Relation type
ENSG00000160714	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10908841	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908842	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908845	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908847	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11265622	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265628	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11265632	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12037271	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12118018	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119111	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12128408	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12136771	0.92[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12407048	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568083	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12740969	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12753666	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12753680	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4345797	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4382717	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4478801	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4584384	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4638123	0.80[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845637	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845638	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845639	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845642	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845647	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5018567	0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6658175	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664608	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6684921	0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6686276	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689965	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6690230	0.82[AMR][1000 genomes]
rs6695045	0.82[AMR][1000 genomes]
rs6700296	0.96[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518694	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7519499	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9660786	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11265621	SHC1	cis	parietal	SCAN
rs11265621	LCE2B	cis	cerebellum	SCAN
rs11265621	EFNA4	cis	parietal	SCAN
rs11265621	CRNN	cis	cerebellum	SCAN
rs11265621	S100A3	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:154427800-154464800	Weak transcription	Ovary	ovary
3	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:154436400-154446400	Weak transcription	NHEK	skin
5	chr1:154436400-154446600	Weak transcription	HMEC	breast
6	chr1:154436600-154446800	Weak transcription	NHDF-Ad	bronchial
7	chr1:154436600-154450600	Weak transcription	HUVEC	blood vessel
8	chr1:154438400-154445800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:154438400-154446000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:154438400-154457800	Weak transcription	Pancreas	Pancrea
11	chr1:154438400-154458400	Weak transcription	Gastric	stomach
12	chr1:154438400-154463400	Weak transcription	Esophagus	oesophagus
13	chr1:154438600-154446800	Weak transcription	NHLF	lung
14	chr1:154438800-154444200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:154438800-154446400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:154438800-154447200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154438800-154450800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:154438800-154454000	Weak transcription	Psoas Muscle	Psoas
19	chr1:154439400-154457600	Weak transcription	Placenta	Placenta
20	chr1:154439600-154443000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr1:154440000-154443000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:154440000-154452800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:154440000-154458200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:154440400-154446400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:154440600-154443000	Strong transcription	Adipose Nuclei	Adipose
26	chr1:154441000-154443000	Strong transcription	Right Ventricle	heart
27	chr1:154441200-154443000	Enhancers	Fetal Brain Male	brain
28	chr1:154441200-154443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:154441200-154450600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:154441400-154450600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:154441400-154451000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:154441600-154443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:154441600-154446400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:154441600-154446600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:154441600-154446600	Weak transcription	Lung	lung
36	chr1:154441600-154447200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:154441600-154449400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:154441600-154451000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:154441600-154451000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:154441600-154465200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:154441800-154443000	Enhancers	Brain Angular Gyrus	brain
42	chr1:154442000-154444200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:154442000-154450600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:154442200-154443000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:154442200-154444000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr1:154442400-154447200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:154442400-154455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:154442400-154455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:154442600-154446600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:154442600-154446600	Weak transcription	Brain Cingulate Gyrus	brain

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