Variant report

Variant	rs2876862
Chromosome Location	chr7:39705273-39705274
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	chr7:39687898..39690458-chr7:39703472..39705888,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11767632	0.95[CEU][hapmap]
rs11769865	0.95[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs11982634	0.95[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2107710	0.95[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2158548	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2158549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2189837	0.89[EUR][1000 genomes]
rs2329464	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823742	0.88[EUR][1000 genomes]
rs4723887	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4723891	0.89[EUR][1000 genomes]
rs4723892	0.90[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462937	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6952363	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6952866	0.92[EUR][1000 genomes]
rs6956681	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6961667	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6969070	0.90[EUR][1000 genomes]
rs6969523	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7785049	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7806651	0.85[EUR][1000 genomes]
rs917077	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2876862	HECW1	cis	parietal	SCAN
rs2876862	LINC00265	cis	lung	GTEx
rs2876862	LINC00265	cis	Thyroid	GTEx
rs2876862	LINC00265	cis	Skin Sun Exposed Lower leg	GTEx
rs2876862	C7orf11	cis	cerebellum	SCAN
rs2876862	RALA	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
2	chr7:39675200-39708800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:39680800-39716400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:39682800-39722000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:39683400-39716600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr7:39683600-39712600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:39687400-39715000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:39690200-39706600	Weak transcription	Fetal Heart	heart
10	chr7:39691800-39707000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr7:39691800-39708800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:39692000-39707000	Weak transcription	Stomach Mucosa	stomach
13	chr7:39692000-39707000	Weak transcription	HSMMtube	muscle
14	chr7:39692000-39707200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:39692200-39714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:39697600-39707000	Weak transcription	Adipose Nuclei	Adipose
17	chr7:39697800-39707000	Weak transcription	HSMM	muscle
18	chr7:39698800-39707000	Weak transcription	Left Ventricle	heart
19	chr7:39699400-39705800	Weak transcription	NHDF-Ad	bronchial
20	chr7:39699400-39707000	Weak transcription	Ovary	ovary
21	chr7:39699400-39712000	Weak transcription	Fetal Kidney	kidney
22	chr7:39699600-39706400	Weak transcription	NHLF	lung
23	chr7:39699600-39707000	Weak transcription	Osteobl	bone
24	chr7:39700000-39707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:39700000-39728200	Weak transcription	Liver	Liver
26	chr7:39701200-39718400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr7:39701800-39708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:39701800-39716400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:39701800-39720800	Weak transcription	Lung	lung
30	chr7:39701800-39721200	Weak transcription	Thymus	Thymus
31	chr7:39701800-39722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
33	chr7:39702000-39705800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:39702000-39706200	Weak transcription	Fetal Stomach	stomach
35	chr7:39702000-39707000	Weak transcription	Right Ventricle	heart
36	chr7:39702000-39709200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:39702000-39716600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:39702000-39727400	Weak transcription	Fetal Intestine Large	intestine
39	chr7:39702200-39706200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:39702200-39706400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:39702200-39716400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:39702400-39706000	Weak transcription	HUVEC	blood vessel
43	chr7:39702600-39707000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:39702800-39706800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:39702800-39707000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr7:39703000-39705800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:39703200-39707000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:39703400-39705800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:39703600-39706200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr7:39703800-39711800	Weak transcription	GM12878-XiMat	blood

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