Variant report

Variant	rs17266491
Chromosome Location	chr6:25516795-25516796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25279560..25282363-chr6:25514276..25517031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1012899	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs169946	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1980453	0.85[CEU][hapmap]
rs2011472	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs212930	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212936	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212938	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs212941	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs214049	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214050	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214064	1.00[JPT][hapmap]
rs214066	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214736	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34164888	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35033684	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35785909	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs391629	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4576241	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711086	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58000836	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392334	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900762	0.86[MEX][hapmap]
rs6903257	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs721803	0.85[CEU][hapmap]
rs926326	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs969297	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10468	chr6:25506093-25519529	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17266491	ZNF193	cis	parietal	SCAN
rs17266491	HIST1H4L	cis	cerebellum	SCAN
rs17266491	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
2	chr6:25463200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:25464200-25518400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:25471600-25597200	Weak transcription	Gastric	stomach
5	chr6:25480800-25523600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:25483000-25532200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:25490400-25521800	Weak transcription	GM12878-XiMat	blood
8	chr6:25490400-25543000	Weak transcription	Hela-S3	cervix
9	chr6:25490600-25524600	Weak transcription	A549	lung
10	chr6:25490800-25521400	Weak transcription	Small Intestine	intestine
11	chr6:25491600-25521000	Weak transcription	HSMMtube	muscle
12	chr6:25494000-25551400	Weak transcription	Left Ventricle	heart
13	chr6:25500600-25520800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:25500600-25523800	Weak transcription	Placenta	Placenta
15	chr6:25504000-25518000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:25506600-25537400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:25506800-25521000	Weak transcription	NHEK	skin
18	chr6:25507600-25525600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:25508800-25521200	Weak transcription	Spleen	Spleen
20	chr6:25509800-25548600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:25510600-25517800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:25511600-25522800	Weak transcription	Primary B cells from cord blood	blood
23	chr6:25511600-25531400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:25512200-25525600	Weak transcription	NHLF	lung
25	chr6:25512800-25521800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:25513200-25517800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:25513800-25519000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:25513800-25524400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:25513800-25530200	Weak transcription	Brain Germinal Matrix	brain
30	chr6:25514000-25525600	Strong transcription	Primary T cells from cord blood	blood
31	chr6:25514200-25542600	Weak transcription	Adipose Nuclei	Adipose
32	chr6:25514200-25558400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:25514400-25523000	Weak transcription	Brain Angular Gyrus	brain
34	chr6:25514400-25541600	Weak transcription	Colonic Mucosa	Colon
35	chr6:25514600-25523800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:25514800-25537800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:25515000-25538600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:25515200-25522000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr6:25515400-25517200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:25515400-25525000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr6:25515600-25517200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr6:25515600-25518000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:25515600-25519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:25515600-25519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:25515600-25523000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr6:25515600-25525600	Strong transcription	Fetal Thymus	thymus
47	chr6:25515800-25516800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:25515800-25516800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:25515800-25516800	Strong transcription	Aorta	Aorta
50	chr6:25515800-25516800	Strong transcription	Lung	lung

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