Variant report

Variant	rs16941855
Chromosome Location	chr17:45381111-45381112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

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

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC040934.1-2	chr17:45380840-45381148	ENSG00000263293.1
2	lnc-AC040934.1-2	chr17:45380832-45381148	ENSG00000263293.1
3	lnc-AC040934.1-2	chr17:45380877-45381148	NONHSAT054295
4	lnc-AC040934.1-2	chr17:45380877-45381148	NONHSAT054297
5	lnc-AC040934.1-2	chr17:45380877-45381148	NONHSAT054296

No data

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867253	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]
rs11867589	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11868344	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868912	0.97[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]
rs11869835	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]
rs11870252	0.97[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];0.97[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]
rs13306478	0.87[AFR][1000 genomes]
rs13306485	0.97[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]
rs16941861	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]
rs16941864	1.00[LWK][hapmap]
rs17605348	1.00[LWK][hapmap]
rs1878067	0.82[CEU][hapmap];0.87[CHB][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292700	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.97[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];0.91[TSI][hapmap];0.92[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41304764	0.88[ASN][1000 genomes]
rs55706706	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56722403	0.97[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];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73322309	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073229	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16941855	EFCAB13	cis	Esophagus Mucosa	GTEx

Chromatin state (count:57 , 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	chr17:45375400-45388400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:45375600-45381600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:45375600-45381800	Strong transcription	Colon Smooth Muscle	Colon
15	chr17:45375800-45381400	Strong transcription	Aorta	Aorta
16	chr17:45375800-45382800	Strong transcription	Fetal Stomach	stomach
17	chr17:45376000-45382600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr17:45376200-45382400	Weak transcription	HSMM	muscle
19	chr17:45376200-45389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:45376400-45381800	Strong transcription	Placenta	Placenta
21	chr17:45376800-45381800	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:45377200-45381600	Strong transcription	Left Ventricle	heart
23	chr17:45377200-45383400	Weak transcription	Pancreas	Pancrea
24	chr17:45377400-45381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:45377600-45381600	Strong transcription	Osteobl	bone
26	chr17:45377800-45381200	Strong transcription	HUVEC	blood vessel
27	chr17:45379000-45382200	Weak transcription	Hela-S3	cervix
28	chr17:45379200-45382600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr17:45379400-45382400	Weak transcription	GM12878-XiMat	blood
30	chr17:45379400-45382600	Weak transcription	K562	blood
31	chr17:45379600-45381400	Strong transcription	Liver	Liver
32	chr17:45379600-45382600	Strong transcription	Fetal Muscle Leg	muscle
33	chr17:45379600-45390400	Weak transcription	Fetal Intestine Small	intestine
34	chr17:45379800-45382400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:45379800-45382400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr17:45379800-45382400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:45379800-45382600	Weak transcription	Right Ventricle	heart
38	chr17:45380000-45381600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:45380000-45381800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:45380000-45382400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:45380000-45382600	Weak transcription	Adipose Nuclei	Adipose
42	chr17:45380200-45382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr17:45380200-45382200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:45380200-45382200	Weak transcription	NHLF	lung
45	chr17:45380200-45382400	Weak transcription	HSMMtube	muscle
46	chr17:45380200-45382400	Weak transcription	NH-A	brain
47	chr17:45380200-45382600	Weak transcription	Fetal Heart	heart
48	chr17:45380200-45382600	Weak transcription	Ovary	ovary
49	chr17:45380200-45382600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr17:45380200-45383000	Weak transcription	Fetal Lung	lung

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