Variant report

Variant	rs2158549
Chromosome Location	chr7:39741925-39741926
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	chr7:39739429..39741292-chr7:39741440..39743225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11767632	0.95[CEU][hapmap]
rs11769865	0.95[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs11982634	0.95[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2107710	0.95[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2158548	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189837	0.93[EUR][1000 genomes]
rs2329464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876862	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]
rs3823742	0.93[EUR][1000 genomes]
rs4723887	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4723891	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4723892	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462937	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs6952363	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6952866	0.89[EUR][1000 genomes]
rs6956681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961667	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6969070	0.89[EUR][1000 genomes]
rs6969523	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7785049	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7806651	0.84[EUR][1000 genomes]
rs917077	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2158549	LINC00265	cis	Thyroid	GTEx
rs2158549	LINC00265	cis	lung	GTEx
rs2158549	HECW1	cis	parietal	SCAN
rs2158549	C7orf11	cis	cerebellum	SCAN
rs2158549	RALA	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
2	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:39729000-39742400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:39730600-39749200	Weak transcription	Ovary	ovary
8	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
9	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:39734200-39746200	Weak transcription	Fetal Kidney	kidney
11	chr7:39734600-39743000	Strong transcription	HSMM	muscle
12	chr7:39735600-39742000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:39735600-39742600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:39735600-39743200	Strong transcription	Primary B cells from cord blood	blood
15	chr7:39735600-39743400	Strong transcription	Primary T cells from cord blood	blood
16	chr7:39736000-39743600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:39736600-39749400	Weak transcription	Fetal Heart	heart
18	chr7:39737200-39743000	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:39737400-39742800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:39737400-39743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:39737400-39749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:39737600-39742400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:39737600-39742600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:39737600-39742800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:39737600-39743200	Strong transcription	NHDF-Ad	bronchial
26	chr7:39737600-39748800	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:39737800-39749400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:39737800-39749400	Weak transcription	Psoas Muscle	Psoas
29	chr7:39738000-39748600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:39738000-39749200	Weak transcription	Fetal Brain Female	brain
31	chr7:39738000-39749400	Weak transcription	Placenta	Placenta
32	chr7:39738400-39743600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr7:39738400-39744400	Weak transcription	HepG2	liver
34	chr7:39738400-39748400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr7:39738600-39744600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:39738600-39748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:39738600-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:39738600-39749200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:39738800-39742200	Weak transcription	Fetal Brain Male	brain
40	chr7:39739600-39742000	Enhancers	HMEC	breast
41	chr7:39739600-39743000	Weak transcription	K562	blood
42	chr7:39739600-39749600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:39739800-39742400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:39740000-39743200	Enhancers	Stomach Mucosa	stomach
45	chr7:39740200-39744800	Weak transcription	Brain Substantia Nigra	brain
46	chr7:39740200-39746200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:39740200-39747200	Weak transcription	Gastric	stomach
48	chr7:39740200-39748000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr7:39740200-39749200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:39740200-39749400	Weak transcription	Pancreas	Pancrea

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