Variant report

Variant	rs10198960
Chromosome Location	chr2:33578010-33578011
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:23)

rs_ID	r²[population]
rs1017677	0.82[CHB][hapmap]
rs10495787	0.80[CHB][hapmap]
rs11885449	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11891105	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11892861	0.92[ASN][1000 genomes]
rs11899010	0.80[CHB][hapmap]
rs17012911	0.85[CHB][hapmap]
rs17012917	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs17012922	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1869449	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs2015189	0.80[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2290426	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2305502	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs28414403	0.84[ASN][1000 genomes]
rs28437398	0.84[ASN][1000 genomes]
rs28709139	0.85[ASN][1000 genomes]
rs34447926	0.85[ASN][1000 genomes]
rs3769549	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3769550	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769552	0.91[ASN][1000 genomes]
rs59867835	0.96[ASN][1000 genomes]
rs6543707	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6719824	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33529800-33609400	Weak transcription	Right Ventricle	heart
2	chr2:33540800-33580800	Weak transcription	Placenta	Placenta
3	chr2:33547600-33579800	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:33547800-33581000	Weak transcription	Fetal Lung	lung
5	chr2:33548200-33588400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:33549000-33588800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:33558400-33592200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:33563000-33579600	Weak transcription	NHDF-Ad	bronchial
9	chr2:33563200-33578200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:33564000-33582200	Weak transcription	Esophagus	oesophagus
11	chr2:33564200-33591600	Weak transcription	Psoas Muscle	Psoas
12	chr2:33565600-33580800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:33565800-33590400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:33565800-33590400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:33566800-33581000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:33568400-33580600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:33570400-33580800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:33570600-33587400	Weak transcription	Fetal Heart	heart
19	chr2:33570800-33588400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:33571000-33590600	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:33571400-33579400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:33571400-33579800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:33571600-33591600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:33572000-33578400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:33572400-33578800	Strong transcription	Osteobl	bone
26	chr2:33572400-33581000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:33572400-33582600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:33573400-33579400	Weak transcription	HUVEC	blood vessel
29	chr2:33574800-33581000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr2:33575000-33581000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:33575200-33580800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:33575600-33580000	Weak transcription	NHLF	lung
33	chr2:33576600-33578600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:33576600-33578600	Strong transcription	Liver	Liver
35	chr2:33576600-33582600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:33577000-33579800	Weak transcription	Ovary	ovary
37	chr2:33577000-33580800	Weak transcription	HSMMtube	muscle
38	chr2:33577200-33578600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:33577400-33578600	Strong transcription	Aorta	Aorta
40	chr2:33577600-33578600	Strong transcription	Fetal Stomach	stomach
41	chr2:33577600-33578800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:33577800-33578800	Strong transcription	NH-A	brain
43	chr2:33578000-33578600	Strong transcription	Left Ventricle	heart
44	chr2:33578000-33581000	Weak transcription	A549	lung

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