Variant report

Variant	rs900610
Chromosome Location	chr12:31816623-31816624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1072778	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10743763	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10771864	0.90[ASN][1000 genomes]
rs10843994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843998	0.91[ASN][1000 genomes]
rs11051539	0.91[ASN][1000 genomes]
rs11051550	0.92[EUR][1000 genomes]
rs1115971	0.94[ASN][1000 genomes]
rs12316119	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2200232	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2374171	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2388926	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs4272863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap]
rs4931537	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7133297	0.94[EUR][1000 genomes]
rs7295568	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];0.88[ASN][1000 genomes]
rs73090337	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309916	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953032	0.94[ASN][1000 genomes]
rs7957042	0.94[ASN][1000 genomes]
rs7966525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968792	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs7970095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980264	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs900609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv522379	chr12:31816623-31817163	Weak transcription Enhancers Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31812800-31818000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:31812800-31818000	Weak transcription	Spleen	Spleen
3	chr12:31812800-31818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:31812800-31819600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:31812800-31823800	Weak transcription	Small Intestine	intestine
6	chr12:31813000-31816800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:31813000-31817200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:31813000-31822000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:31813000-31822000	Weak transcription	NH-A	brain
10	chr12:31813000-31826000	Weak transcription	Gastric	stomach
11	chr12:31813200-31816800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:31813200-31817000	Weak transcription	Fetal Kidney	kidney
13	chr12:31813200-31818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:31813200-31818000	Weak transcription	Placenta	Placenta
15	chr12:31813200-31818400	Weak transcription	Esophagus	oesophagus
16	chr12:31813200-31822000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:31813200-31837000	Weak transcription	Fetal Brain Male	brain
18	chr12:31813400-31816800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:31813400-31818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:31813400-31820600	Weak transcription	HSMMtube	muscle
21	chr12:31813400-31820800	Weak transcription	Ovary	ovary
22	chr12:31813400-31821600	Weak transcription	Thymus	Thymus
23	chr12:31813400-31821800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:31813400-31821800	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:31813400-31821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:31813400-31821800	Weak transcription	Fetal Lung	lung
27	chr12:31813400-31822000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:31813400-31822000	Weak transcription	Brain Anterior Caudate	brain
29	chr12:31813400-31822000	Weak transcription	Fetal Intestine Large	intestine
30	chr12:31813400-31822000	Weak transcription	Psoas Muscle	Psoas
31	chr12:31813400-31822000	Weak transcription	Right Ventricle	heart
32	chr12:31813400-31822200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:31813400-31822200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:31813400-31825200	Weak transcription	Aorta	Aorta
35	chr12:31813400-31825400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:31813400-31825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:31813400-31826600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:31813400-31835200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:31813400-31835600	Weak transcription	Brain Angular Gyrus	brain
40	chr12:31813400-31836200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:31813600-31817000	Weak transcription	K562	blood
42	chr12:31813600-31818200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr12:31813600-31821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:31813800-31821800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:31814200-31821800	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:31814200-31821800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:31814800-31817200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:31814800-31817200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:31815000-31817400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:31815200-31822000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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