Variant report

Variant	rs3772540
Chromosome Location	chr3:105403010-105403011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10460808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1075739	0.82[CEU][hapmap]
rs12637560	0.82[CEU][hapmap]
rs12637809	0.82[CEU][hapmap]
rs16844736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851563	0.82[CEU][hapmap]
rs16851587	0.82[CEU][hapmap]
rs16851630	0.82[CEU][hapmap]
rs1992521	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028597	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2301036	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57735492	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7641825	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs7649466	0.87[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877307	chr3:105373836-105465189	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv591242	chr3:105373836-105470134	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:105373800-105406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:105375800-105405000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
6	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
7	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:105378000-105420800	Weak transcription	HUVEC	blood vessel
10	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:105378600-105438600	Weak transcription	Spleen	Spleen
12	chr3:105379000-105437400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:105379200-105440400	Weak transcription	Thymus	Thymus
14	chr3:105380600-105411800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:105382200-105404800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:105382400-105405000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:105382800-105404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:105384600-105404600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:105385000-105404600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:105385200-105404400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:105385400-105405200	Strong transcription	Osteobl	bone
22	chr3:105385400-105411000	Weak transcription	HMEC	breast
23	chr3:105385600-105404400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:105385600-105404400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:105385800-105404400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:105387200-105420800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:105388400-105421000	Weak transcription	Gastric	stomach
28	chr3:105388600-105419800	Weak transcription	Brain Germinal Matrix	brain
29	chr3:105389000-105407200	Weak transcription	HepG2	liver
30	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
31	chr3:105390800-105403600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:105390800-105404600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:105390800-105406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:105391200-105404600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:105392200-105403200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:105392200-105404400	Strong transcription	Placenta	Placenta
37	chr3:105392600-105404200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:105393600-105420800	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:105393800-105405000	Weak transcription	Aorta	Aorta
40	chr3:105394200-105405200	Weak transcription	A549	lung
41	chr3:105394200-105438800	Weak transcription	NHEK	skin
42	chr3:105395200-105403800	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:105395200-105404400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:105395800-105403800	Weak transcription	Esophagus	oesophagus
45	chr3:105396000-105411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:105396000-105420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:105396000-105420800	Weak transcription	Brain Angular Gyrus	brain
48	chr3:105396000-105432600	Weak transcription	Pancreas	Pancrea
49	chr3:105396000-105437200	Weak transcription	Psoas Muscle	Psoas
50	chr3:105396000-105437400	Weak transcription	Brain Cingulate Gyrus	brain

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