Variant report

Variant	rs17252870
Chromosome Location	chr6:25494666-25494667
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1028319	0.81[AMR][1000 genomes]
rs11969981	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12526321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528159	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17253044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17491869	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064128	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs214055	0.80[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2294344	1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs301393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676593	0.81[AMR][1000 genomes]
rs3788994	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3804133	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4419666	1.00[YRI][hapmap]
rs447724	1.00[ASN][1000 genomes]
rs4711085	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4712950	1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs57141743	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61340952	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72839025	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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
2	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
3	nsv432856	chr6:25468825-25494666	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17252870	HIST1H3D	cis	parietal	SCAN
rs17252870	TDP2	cis	parietal	SCAN
rs17252870	KAAG1	cis	parietal	SCAN
rs17252870	ZSCAN23	cis	cerebellum	SCAN
rs17252870	PRSS16	cis	parietal	SCAN
rs17252870	HIST1H3E	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25446800-25504400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:25449400-25515800	Weak transcription	Lung	lung
3	chr6:25456400-25499200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:25456400-25515800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
6	chr6:25463200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:25464000-25498800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:25464200-25518400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:25465400-25499000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:25466400-25516000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:25466800-25515800	Weak transcription	Fetal Stomach	stomach
12	chr6:25471600-25597200	Weak transcription	Gastric	stomach
13	chr6:25473400-25495400	Weak transcription	Pancreas	Pancrea
14	chr6:25473600-25499600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:25473600-25516000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:25476800-25499800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:25477800-25499600	Weak transcription	NHLF	lung
18	chr6:25477800-25499800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:25478000-25499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:25478000-25499200	Weak transcription	NHEK	skin
21	chr6:25480000-25511400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:25480800-25523600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:25483000-25532200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:25483800-25499000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:25484000-25500000	Weak transcription	HMEC	breast
26	chr6:25484600-25505800	Weak transcription	Aorta	Aorta
27	chr6:25484800-25498200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:25484800-25515600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:25486400-25501600	Weak transcription	Fetal Brain Male	brain
30	chr6:25487600-25499600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:25488800-25497600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:25489000-25498800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:25490400-25494800	Weak transcription	Liver	Liver
34	chr6:25490400-25496000	Weak transcription	Stomach Mucosa	stomach
35	chr6:25490400-25497400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:25490400-25499000	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:25490400-25515800	Weak transcription	Thymus	Thymus
38	chr6:25490400-25521800	Weak transcription	GM12878-XiMat	blood
39	chr6:25490400-25543000	Weak transcription	Hela-S3	cervix
40	chr6:25490600-25524600	Weak transcription	A549	lung
41	chr6:25490800-25495400	Weak transcription	Adipose Nuclei	Adipose
42	chr6:25490800-25500000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:25490800-25500600	Weak transcription	Fetal Intestine Large	intestine
44	chr6:25490800-25506400	Weak transcription	Fetal Intestine Small	intestine
45	chr6:25490800-25511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:25490800-25515800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr6:25490800-25515800	Weak transcription	Ovary	ovary
48	chr6:25490800-25516400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:25490800-25521400	Weak transcription	Small Intestine	intestine
50	chr6:25491000-25495600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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