Variant report

Variant	rs960887
Chromosome Location	chr8:121048383-121048384
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	chr8:121048344..121050825-chr8:121050887..121053593,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL14A1-2	chr8:121048080-121049710	NONHSAT128446

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10090001	0.82[EUR][1000 genomes]
rs10095205	0.95[EUR][1000 genomes]
rs10095532	0.95[EUR][1000 genomes]
rs10101620	0.82[EUR][1000 genomes]
rs10101943	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10505376	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10808506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10955948	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11780912	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11780985	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11996625	0.81[ASN][1000 genomes]
rs12114445	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12386849	0.85[ASN][1000 genomes]
rs12542032	0.85[ASN][1000 genomes]
rs12542895	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12543907	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12545676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548223	0.90[JPT][hapmap]
rs12548273	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1401811	0.85[ASN][1000 genomes]
rs1519807	0.89[EUR][1000 genomes]
rs1519808	0.89[EUR][1000 genomes]
rs1519812	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1519813	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[EUR][1000 genomes]
rs16893478	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16893517	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16893536	0.80[JPT][hapmap]
rs16893570	0.80[JPT][hapmap]
rs17226296	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17822044	0.90[JPT][hapmap]
rs1973732	0.81[ASN][1000 genomes]
rs1980228	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2292946	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2326431	0.81[ASN][1000 genomes]
rs28530768	0.95[EUR][1000 genomes]
rs2875928	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs2875931	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4871825	0.84[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4871828	0.85[EUR][1000 genomes]
rs56702755	0.81[EUR][1000 genomes]
rs57868486	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60717250	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60754245	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6469894	0.86[EUR][1000 genomes]
rs6469895	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6469897	0.84[EUR][1000 genomes]
rs66490854	0.85[EUR][1000 genomes]
rs66507952	0.88[ASN][1000 genomes]
rs66608823	0.85[ASN][1000 genomes]
rs66614869	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67872361	0.92[EUR][1000 genomes]
rs6980708	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6981402	0.86[ASN][1000 genomes]
rs6986231	0.81[EUR][1000 genomes]
rs6993924	0.85[EUR][1000 genomes]
rs6998730	0.82[EUR][1000 genomes]
rs7000436	0.81[YRI][hapmap]
rs7004815	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7005228	0.82[EUR][1000 genomes]
rs7007998	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7013298	0.81[CEU][hapmap];0.88[CHD][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs7016816	0.80[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs72675741	0.89[ASN][1000 genomes]
rs73315941	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7813041	0.80[ASN][1000 genomes]
rs7816925	0.80[JPT][hapmap]
rs7817016	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs7817522	0.85[ASN][1000 genomes]
rs7821947	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs7822662	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7822927	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7824793	0.81[EUR][1000 genomes]
rs7829101	0.96[CEU][hapmap];0.85[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs7829116	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7830028	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7833073	0.81[CEU][hapmap];0.88[CHD][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs7836087	0.81[CEU][hapmap];0.85[CHD][hapmap];0.85[EUR][1000 genomes]
rs7840217	0.80[JPT][hapmap]
rs7841230	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7841621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7843503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955293	0.88[CHD][hapmap];0.81[MEX][hapmap];0.85[EUR][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	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs960887	RP11-760H22.2	cis	Adipose Subcutaneous	GTEx
rs960887	DEPDC6	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
2	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
3	chr8:121022800-121053000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr8:121029800-121048400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr8:121032000-121058000	Weak transcription	Pancreas	Pancrea
6	chr8:121036000-121063800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr8:121038400-121061800	Weak transcription	Adipose Nuclei	Adipose
8	chr8:121042000-121063400	Weak transcription	Spleen	Spleen
9	chr8:121044800-121049000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:121044800-121049400	Enhancers	Osteobl	bone
11	chr8:121044800-121050000	Enhancers	Ovary	ovary
12	chr8:121045000-121056600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:121045200-121053400	Weak transcription	Liver	Liver
14	chr8:121045400-121049400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:121046000-121048400	Enhancers	Colon Smooth Muscle	Colon
16	chr8:121046000-121049400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr8:121046200-121053000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr8:121046200-121053200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr8:121046200-121065200	Weak transcription	Psoas Muscle	Psoas
20	chr8:121046400-121056600	Weak transcription	Gastric	stomach
21	chr8:121046600-121052800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:121047000-121050000	Enhancers	Rectal Smooth Muscle	rectum
23	chr8:121047200-121048800	Enhancers	Fetal Muscle Leg	muscle
24	chr8:121047200-121049000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr8:121047600-121048600	Enhancers	Stomach Smooth Muscle	stomach
26	chr8:121047800-121048400	Enhancers	Fetal Kidney	kidney
27	chr8:121047800-121048600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr8:121047800-121048800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr8:121047800-121049400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:121048000-121048400	Enhancers	Fetal Intestine Small	intestine
31	chr8:121048000-121048600	Enhancers	Fetal Intestine Large	intestine
32	chr8:121048000-121048800	Enhancers	Brain Cingulate Gyrus	brain
33	chr8:121048000-121048800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr8:121048000-121048800	Enhancers	Stomach Mucosa	stomach
35	chr8:121048000-121049000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr8:121048000-121049000	Enhancers	Brain Angular Gyrus	brain
37	chr8:121048000-121049000	Enhancers	Brain Hippocampus Middle	brain
38	chr8:121048000-121049000	Enhancers	Brain Substantia Nigra	brain
39	chr8:121048000-121049200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr8:121048000-121049200	Enhancers	Fetal Lung	lung
41	chr8:121048000-121049200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr8:121048000-121049800	Enhancers	Fetal Stomach	stomach
43	chr8:121048200-121048400	Enhancers	Placenta	Placenta
44	chr8:121048200-121048400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr8:121048200-121048600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr8:121048200-121048800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr8:121048200-121048800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr8:121048200-121048800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr8:121048200-121048800	Enhancers	Esophagus	oesophagus
50	chr8:121048200-121049000	Enhancers	Cortex derived primary cultured neurospheres	brain

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