Variant report

Variant	rs11869835
Chromosome Location	chr17:45381823-45381824
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45375988..45378357-chr17:45379217..45383019,3	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11079771	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11867192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867589	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11868344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868912	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11869439	1.00[JPT][hapmap]
rs11869768	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11870252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11870781	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871031	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11871477	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12051664	1.00[JPT][hapmap]
rs12051702	1.00[JPT][hapmap]
rs12162128	0.98[ASN][1000 genomes]
rs13306485	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16941751	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs16941771	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16941855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878067	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292700	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785870	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3785873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41304764	0.88[ASN][1000 genomes]
rs55706706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56722403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5919	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73322309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073229	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11869835	EFCAB13	cis	Skin Sun Exposed Lower leg	GTEx
rs11869835	C17orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
2	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:45371400-45393000	Weak transcription	Dnd41	blood
4	chr17:45372400-45383600	Weak transcription	Gastric	stomach
5	chr17:45372400-45389600	Weak transcription	Esophagus	oesophagus
6	chr17:45372400-45389800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:45372400-45394400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:45372800-45382800	Weak transcription	Colonic Mucosa	Colon
9	chr17:45373600-45382600	Weak transcription	Spleen	Spleen
10	chr17:45374000-45392800	Weak transcription	Brain Substantia Nigra	brain
11	chr17:45375400-45388400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:45375800-45382800	Strong transcription	Fetal Stomach	stomach
13	chr17:45376000-45382600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr17:45376200-45382400	Weak transcription	HSMM	muscle
15	chr17:45376200-45389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:45377200-45383400	Weak transcription	Pancreas	Pancrea
17	chr17:45379000-45382200	Weak transcription	Hela-S3	cervix
18	chr17:45379200-45382600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr17:45379400-45382400	Weak transcription	GM12878-XiMat	blood
20	chr17:45379400-45382600	Weak transcription	K562	blood
21	chr17:45379600-45382600	Strong transcription	Fetal Muscle Leg	muscle
22	chr17:45379600-45390400	Weak transcription	Fetal Intestine Small	intestine
23	chr17:45379800-45382400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr17:45379800-45382400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr17:45379800-45382400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:45379800-45382600	Weak transcription	Right Ventricle	heart
27	chr17:45380000-45382400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:45380000-45382600	Weak transcription	Adipose Nuclei	Adipose
29	chr17:45380200-45382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr17:45380200-45382200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:45380200-45382200	Weak transcription	NHLF	lung
32	chr17:45380200-45382400	Weak transcription	HSMMtube	muscle
33	chr17:45380200-45382400	Weak transcription	NH-A	brain
34	chr17:45380200-45382600	Weak transcription	Fetal Heart	heart
35	chr17:45380200-45382600	Weak transcription	Ovary	ovary
36	chr17:45380200-45382600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr17:45380200-45383000	Weak transcription	Fetal Lung	lung
38	chr17:45380200-45392800	Weak transcription	Brain Hippocampus Middle	brain
39	chr17:45380400-45382200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:45380400-45387800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr17:45381200-45383800	Enhancers	NHDF-Ad	bronchial
42	chr17:45381400-45382000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:45381400-45382400	Weak transcription	Aorta	Aorta
44	chr17:45381400-45383800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:45381400-45392600	Weak transcription	Liver	Liver
46	chr17:45381600-45382400	Weak transcription	Osteobl	bone
47	chr17:45381600-45382600	Enhancers	HUVEC	blood vessel
48	chr17:45381600-45383800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:45381600-45384000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr17:45381600-45384400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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