Variant report

Variant	rs12485249
Chromosome Location	chr3:114055345-114055346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10934262	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10934268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11915585	1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918680	1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12493360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12496777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354348	1.00[JPT][hapmap]
rs16822393	1.00[JPT][hapmap]
rs2466358	1.00[EUR][1000 genomes]
rs2654754	1.00[JPT][hapmap]
rs2654763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2733397	1.00[CHB][hapmap]
rs3732783	1.00[JPT][hapmap]
rs4682534	1.00[JPT][hapmap]
rs4682539	1.00[CHB][hapmap]
rs9288991	1.00[JPT][hapmap]
rs9859762	1.00[JPT][hapmap]

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	nsv948596	chr3:113852666-114434158	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv428094	chr3:113983846-114128496	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv829679	chr3:114049928-114252735	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:114025600-114057000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:114027400-114057000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:114030000-114057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:114032800-114057000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:114033800-114057000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:114034200-114068800	Weak transcription	Gastric	stomach
7	chr3:114034400-114057800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:114035600-114057000	Weak transcription	Fetal Stomach	stomach
9	chr3:114035800-114057000	Weak transcription	NHLF	lung
10	chr3:114035800-114057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:114035800-114069400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:114037000-114057600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:114037600-114057000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:114037600-114057000	Weak transcription	Ovary	ovary
15	chr3:114039000-114057000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:114039000-114067400	Weak transcription	Fetal Kidney	kidney
17	chr3:114039000-114070000	Weak transcription	NH-A	brain
18	chr3:114039000-114082400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:114039200-114099000	Weak transcription	Hela-S3	cervix
20	chr3:114040400-114057000	Weak transcription	Lung	lung
21	chr3:114040400-114057000	Weak transcription	Pancreas	Pancrea
22	chr3:114040400-114057000	Weak transcription	Right Ventricle	heart
23	chr3:114040800-114064800	Strong transcription	HSMM	muscle
24	chr3:114041200-114068200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:114042400-114057800	Weak transcription	Spleen	Spleen
26	chr3:114043000-114061800	Weak transcription	Small Intestine	intestine
27	chr3:114044600-114057600	Weak transcription	Thymus	Thymus
28	chr3:114044600-114057800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:114044800-114074200	Weak transcription	Psoas Muscle	Psoas
30	chr3:114045000-114057000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:114045400-114068200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:114047200-114069200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:114048000-114057800	Weak transcription	Osteobl	bone
34	chr3:114048200-114057000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:114049400-114057000	Weak transcription	Brain Germinal Matrix	brain
36	chr3:114050200-114056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:114050200-114057000	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:114050400-114057000	Weak transcription	Aorta	Aorta
39	chr3:114050400-114057000	Weak transcription	Fetal Intestine Large	intestine
40	chr3:114050400-114057000	Weak transcription	Fetal Intestine Small	intestine
41	chr3:114050400-114068800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:114050600-114057000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:114050600-114057800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:114050600-114089400	Weak transcription	HepG2	liver
45	chr3:114051000-114068600	Weak transcription	Fetal Brain Female	brain
46	chr3:114051200-114055600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:114051200-114057000	Weak transcription	Primary T cells from cord blood	blood
48	chr3:114051400-114055600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:114051400-114055800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr3:114051400-114057000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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