Variant report

Variant	rs9653930
Chromosome Location	chr3:135810314-135810315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512990	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12330335	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12695644	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13068210	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13079205	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081671	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13082532	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1393786	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1393787	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1403763	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28509770	0.81[EUR][1000 genomes]
rs28519617	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28535121	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28669017	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34864445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35320690	1.00[CEU][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35352346	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3905668	0.81[EUR][1000 genomes]
rs56398805	0.81[EUR][1000 genomes]
rs6439629	1.00[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67109185	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67589653	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6769762	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6775778	0.95[CEU][hapmap]
rs6786582	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6792630	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793835	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799056	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799517	0.81[EUR][1000 genomes]
rs9827662	0.89[CEU][hapmap]
rs9834966	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848926	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870122	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9881400	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS 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	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135790200-135830800	Weak transcription	Psoas Muscle	Psoas
2	chr3:135800400-135815400	Strong transcription	Stomach Smooth Muscle	stomach
3	chr3:135803000-135826600	Weak transcription	Liver	Liver
4	chr3:135803400-135848000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:135803600-135821600	Weak transcription	Right Ventricle	heart
6	chr3:135803600-135860600	Weak transcription	Esophagus	oesophagus
7	chr3:135803800-135832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:135803800-135860000	Weak transcription	NHLF	lung
9	chr3:135804000-135814800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:135804000-135832000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:135804000-135833200	Weak transcription	HMEC	breast
12	chr3:135804200-135819400	Weak transcription	Colonic Mucosa	Colon
13	chr3:135804600-135811400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:135804600-135822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:135805000-135813200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:135805200-135832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:135805200-135832800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:135805400-135843800	Weak transcription	NHEK	skin
19	chr3:135806000-135812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:135806600-135810400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr3:135806600-135810600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:135806600-135812000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:135807000-135811400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:135807200-135822000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:135807400-135833200	Weak transcription	Lung	lung
26	chr3:135808600-135810400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:135808800-135813000	Strong transcription	Fetal Lung	lung
28	chr3:135808800-135814800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:135809000-135810400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:135809000-135810400	Strong transcription	Fetal Heart	heart
31	chr3:135809000-135810400	Strong transcription	NHDF-Ad	bronchial
32	chr3:135809000-135812800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:135809200-135810400	Strong transcription	Fetal Intestine Large	intestine
34	chr3:135809200-135816400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:135809400-135810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:135809400-135810400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:135809400-135810400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:135809400-135810400	Strong transcription	Adipose Nuclei	Adipose
39	chr3:135809400-135810400	Strong transcription	Brain Germinal Matrix	brain
40	chr3:135809400-135810400	Strong transcription	Brain Substantia Nigra	brain
41	chr3:135809400-135810400	Strong transcription	HSMMtube	muscle
42	chr3:135809400-135810600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:135809400-135810600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:135809400-135810600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:135809400-135811000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:135809400-135812800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:135809400-135814000	Strong transcription	HSMM	muscle
48	chr3:135809400-135815000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:135809600-135810400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:135809600-135810400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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