Variant report

Variant	rs301377
Chromosome Location	chr6:25516745-25516746
allele	C/T
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: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10456322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752017	1.00[JPT][hapmap]
rs11759560	1.00[JPT][hapmap]
rs11759648	1.00[JPT][hapmap]
rs12191432	1.00[JPT][hapmap]
rs12192331	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192342	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12195457	1.00[JPT][hapmap]
rs12203031	1.00[JPT][hapmap]
rs12203442	1.00[JPT][hapmap]
rs12207668	0.83[EUR][1000 genomes]
rs12207791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12208868	1.00[JPT][hapmap]
rs12211739	1.00[JPT][hapmap]
rs12214693	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1410443	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs150533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884575	1.00[JPT][hapmap]
rs212927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212929	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs212931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212935	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs212937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212939	0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs212940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762357	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs301376	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301388	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs441472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443641	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453181	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs485567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55633691	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55883446	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56285037	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56383372	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6902158	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs6927384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716796	1.00[JPT][hapmap]
rs72839082	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72839085	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72839087	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72839088	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72839089	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760865	1.00[JPT][hapmap]
rs7738866	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7762537	1.00[JPT][hapmap]
rs7764258	1.00[JPT][hapmap]
rs9348685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9379774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461151	1.00[JPT][hapmap]
rs9461190	1.00[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs301377	HIST1H2AM	cis	cerebellum	SCAN
rs301377	LRRC16	cis	lesional skin	skin_eQTL

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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