Variant report

Variant	rs3785873
Chromosome Location	chr17:45379238-45379239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45369846..45373285-chr17:45374240..45379330,4	K562	blood:
2	chr17:45375988..45378357-chr17:45379217..45383019,3	K562	blood:
3	chr17:45372166..45375464-chr17:45377689..45379653,5	K562	blood:
4	chr17:45307160..45307858-chr17:45378806..45379663,2	K562	blood:
5	chr17:45377393..45380597-chr17:45384667..45388953,5	K562	blood:
6	chr17:45373943..45375464-chr17:45378021..45379653,2	K562	blood:
7	chr17:45377393..45379681-chr17:45383404..45387690,4	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	0.94[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[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]
rs11867589	0.80[CHB][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];1.00[JPT][hapmap]
rs11869835	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]
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];0.93[CHB][hapmap];0.86[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];1.00[JPT][hapmap]
rs11871477	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs12051664	0.80[CHB][hapmap];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];1.00[JPT][hapmap]
rs16941855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292700	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785870	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[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];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];0.95[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
rs3785873	EFCAB13	cis	Skin Sun Exposed Lower leg	GTEx
rs3785873	C17orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 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	chr17:45372800-45381400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:45372800-45382800	Weak transcription	Colonic Mucosa	Colon
10	chr17:45373600-45382600	Weak transcription	Spleen	Spleen
11	chr17:45374000-45392800	Weak transcription	Brain Substantia Nigra	brain
12	chr17:45374400-45379400	Weak transcription	Brain Hippocampus Middle	brain
13	chr17:45375400-45388400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr17:45375600-45381600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:45375600-45381800	Strong transcription	Colon Smooth Muscle	Colon
16	chr17:45375800-45379800	Strong transcription	Rectal Smooth Muscle	rectum
17	chr17:45375800-45381400	Strong transcription	Aorta	Aorta
18	chr17:45375800-45382800	Strong transcription	Fetal Stomach	stomach
19	chr17:45376000-45382600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr17:45376200-45382400	Weak transcription	HSMM	muscle
21	chr17:45376200-45389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:45376400-45381800	Strong transcription	Placenta	Placenta
23	chr17:45376800-45381800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr17:45377200-45381000	Strong transcription	NHDF-Ad	bronchial
25	chr17:45377200-45381600	Strong transcription	Left Ventricle	heart
26	chr17:45377200-45383400	Weak transcription	Pancreas	Pancrea
27	chr17:45377400-45379600	Weak transcription	Liver	Liver
28	chr17:45377400-45381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:45377600-45381600	Strong transcription	Osteobl	bone
30	chr17:45377800-45380200	Strong transcription	Ovary	ovary
31	chr17:45377800-45380400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:45377800-45381200	Strong transcription	HUVEC	blood vessel
33	chr17:45378000-45379400	Enhancers	K562	blood
34	chr17:45378000-45380000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:45378200-45379800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr17:45378200-45381000	Weak transcription	Fetal Intestine Large	intestine
37	chr17:45378800-45379400	Weak transcription	Right Ventricle	heart
38	chr17:45378800-45379600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr17:45378800-45379600	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr17:45378800-45380000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:45379000-45379400	ZNF genes & repeats	Fetal Heart	heart
42	chr17:45379000-45379400	Enhancers	GM12878-XiMat	blood
43	chr17:45379000-45380000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:45379000-45382200	Weak transcription	Hela-S3	cervix
45	chr17:45379200-45379600	ZNF genes & repeats	NHLF	lung
46	chr17:45379200-45379800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:45379200-45379800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:45379200-45379800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
49	chr17:45379200-45380000	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr17:45379200-45380200	Strong transcription	Fetal Lung	lung

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