Variant report

Variant	rs12330209
Chromosome Location	chr3:113020075-113020076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1082588	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1082589	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12330211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471883	0.89[CEU][hapmap]
rs1471884	0.90[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs2270782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270783	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291905	0.86[ASW][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs2936812	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4396864	0.89[CEU][hapmap]
rs6438137	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6769604	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs6783479	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793192	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801402	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712530	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618847	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623919	0.89[CEU][hapmap]
rs7637618	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7646188	0.90[CEU][hapmap]
rs775214	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775215	0.95[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775217	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs808949	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808950	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs810209	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852703	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
3	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
5	chr3:112995400-113035800	Weak transcription	Lung	lung
6	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
7	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
8	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
11	chr3:112998600-113036000	Weak transcription	Gastric	stomach
12	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
14	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
15	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
18	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
19	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
20	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
21	chr3:113006800-113022600	Weak transcription	Hela-S3	cervix
22	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:113007000-113022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:113007000-113022600	Weak transcription	Liver	Liver
25	chr3:113007000-113022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:113007000-113034400	Weak transcription	HSMM	muscle
29	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:113008000-113023600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:113008400-113023800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:113009000-113032800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:113010800-113022000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:113010800-113022600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:113010800-113031000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:113010800-113031400	Weak transcription	Fetal Stomach	stomach
39	chr3:113010800-113034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:113010800-113034400	Weak transcription	Fetal Lung	lung
41	chr3:113010800-113035800	Weak transcription	Ovary	ovary
42	chr3:113011000-113036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:113011400-113022000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:113011600-113034000	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:113012800-113022600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:113013600-113020400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:113013600-113022400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:113013600-113034400	Weak transcription	A549	lung
49	chr3:113013600-113065200	Weak transcription	Left Ventricle	heart
50	chr3:113014400-113022400	Weak transcription	Primary T cells from cord blood	blood

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