Variant report

Variant	rs12192517
Chromosome Location	chr6:25342609-25342610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10946768	0.81[JPT][hapmap]
rs12193883	0.90[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1569558	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16890409	0.81[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2328853	0.92[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs34283429	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712910	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4712911	0.84[ASN][1000 genomes]
rs4712915	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4712916	0.89[ASN][1000 genomes]
rs4712917	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs5013971	0.83[ASN][1000 genomes]
rs73399941	0.82[ASN][1000 genomes]
rs9393641	0.92[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25332000-25346800	Weak transcription	Ovary	ovary
2	chr6:25333200-25343800	Enhancers	Fetal Intestine Small	intestine
3	chr6:25333800-25346400	Weak transcription	Left Ventricle	heart
4	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
5	chr6:25336400-25342800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:25336800-25344000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:25336800-25350200	Weak transcription	Lung	lung
8	chr6:25336800-25354600	Weak transcription	Right Atrium	heart
9	chr6:25337000-25342800	Weak transcription	Primary T cells from cord blood	blood
10	chr6:25337000-25343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:25337400-25357800	Weak transcription	NHEK	skin
12	chr6:25337600-25343800	Enhancers	Fetal Intestine Large	intestine
13	chr6:25338800-25343000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:25339600-25346200	Weak transcription	Fetal Lung	lung
15	chr6:25340000-25343000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr6:25340000-25349400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:25340400-25343600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:25340400-25344000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:25340600-25342800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:25340800-25343400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:25340800-25344800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:25341000-25343400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:25341000-25343800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:25341000-25352800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
26	chr6:25341200-25343000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr6:25341200-25343000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:25341400-25343400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:25341400-25343800	Weak transcription	Aorta	Aorta
30	chr6:25341400-25345800	Weak transcription	Gastric	stomach
31	chr6:25341600-25344800	Weak transcription	Stomach Mucosa	stomach
32	chr6:25342000-25342800	Enhancers	H9 Cell Line	embryonic stem cell
33	chr6:25342000-25342800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:25342000-25343800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:25342200-25343600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:25342200-25343800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:25342200-25346400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:25342400-25342800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:25342400-25342800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:25342400-25343600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr6:25342400-25343800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:25342400-25344000	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:25342400-25344000	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:25342400-25345600	Weak transcription	Small Intestine	intestine
45	chr6:25342400-25346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:25342400-25350600	Weak transcription	HSMMtube	muscle
47	chr6:25342600-25342800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:25342600-25342800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr6:25342600-25343400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:25342600-25343400	Enhancers	HMEC	breast

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