Variant report

Variant	rs9867864
Chromosome Location	chr3:116498-116499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11130301	0.80[ASN][1000 genomes]
rs12487203	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs1516331	0.81[ASN][1000 genomes]
rs1516333	0.83[ASN][1000 genomes]
rs1568094	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568095	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17030598	0.83[ASN][1000 genomes]
rs17044761	0.87[ASN][1000 genomes]
rs17050452	0.90[ASN][1000 genomes]
rs35713901	0.86[ASN][1000 genomes]
rs4685768	0.94[ASN][1000 genomes]
rs4685781	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59653430	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60858966	0.83[ASN][1000 genomes]
rs6775203	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73013034	0.89[ASN][1000 genomes]
rs7611700	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs908477	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9311804	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs954824	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9852028	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861004	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs990284	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:128 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876281	chr3:60001-188865	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv876282	chr3:60001-211745	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1010627	chr3:60333-116590	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1008330	chr3:60333-123305	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1012781	chr3:60333-123514	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1000608	chr3:60333-126209	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1007799	chr3:60333-127933	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1002577	chr3:60333-134991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1005233	chr3:60333-140727	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1000721	chr3:60333-141216	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1001171	chr3:60333-142682	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1006027	chr3:60333-143719	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv998594	chr3:60333-144832	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1003910	chr3:60333-145723	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1004219	chr3:60333-146045	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1003412	chr3:60333-147115	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1012315	chr3:60333-147520	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1008987	chr3:60333-151789	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv997387	chr3:60333-152047	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1014700	chr3:60333-152606	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1010822	chr3:60333-157553	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1001399	chr3:60333-168827	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv1000510	chr3:60333-172906	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1002045	chr3:60333-175348	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1010197	chr3:60333-187375	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv1008998	chr3:60333-202034	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv997648	chr3:60333-206118	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	nsv1005220	chr3:60333-237868	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv1008604	chr3:60333-368771	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
30	nsv1010433	chr3:60333-480173	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
31	esv2763748	chr3:60345-128189	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
32	nsv460290	chr3:63411-120321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
33	nsv460291	chr3:63411-120321	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
34	nsv589231	chr3:63411-120321	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
35	nsv460292	chr3:63411-126158	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
36	nsv589232	chr3:63411-126158	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
37	nsv589233	chr3:63411-128697	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv516303	chr3:63411-133412	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
39	nsv460293	chr3:63411-185281	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
40	nsv589234	chr3:63411-185281	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
41	nsv469898	chr3:63411-928456	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
42	nsv1002126	chr3:66011-142682	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
43	nsv997453	chr3:66011-145723	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
44	nsv1008169	chr3:66011-151789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
45	nsv1013078	chr3:66011-168827	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
46	nsv1007289	chr3:66011-173714	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
47	nsv1011475	chr3:66011-185536	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
48	nsv1009462	chr3:66011-186199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
49	nsv998095	chr3:66011-202034	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
50	nsv1004245	chr3:66011-252344	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9867864	CHL1	cis	Muscle Skeletal	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112800-117200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:112800-117200	Enhancers	Adipose Nuclei	Adipose
3	chr3:113000-118000	Enhancers	Brain Germinal Matrix	brain
4	chr3:113400-118000	Enhancers	Fetal Lung	lung
5	chr3:113800-117200	Enhancers	Ovary	ovary
6	chr3:113800-117600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:113800-118200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:114400-117000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:115200-116600	Weak transcription	Right Atrium	heart
10	chr3:115400-116600	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:115600-116600	Weak transcription	Fetal Brain Female	brain
12	chr3:115600-123600	Weak transcription	Fetal Brain Male	brain
13	chr3:115800-116800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:115800-117000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:116000-117000	Enhancers	Rectal Smooth Muscle	rectum
16	chr3:116400-117200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:116400-117200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:116400-117400	Enhancers	Fetal Stomach	stomach

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