Variant report

Variant	rs7163840
Chromosome Location	chr15:83398303-83398304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83396804..83398373-chr15:83475659..83477740,2	MCF-7	breast:
2	chr15:83287250..83289710-chr15:83397763..83399653,2	K562	blood:
3	chr15:83396843..83399446-chr15:83416836..83419742,3	MCF-7	breast:
4	chr15:83397915..83402775-chr15:83404352..83408497,6	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction
ENSG00000259315	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1105867	0.91[JPT][hapmap]
rs1145170	0.87[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs1259176	0.91[CEU][hapmap]
rs12908713	0.87[CEU][hapmap]
rs1313494	0.86[CEU][hapmap]
rs1553885	0.87[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1877241	0.91[JPT][hapmap]
rs1971554	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2567632	0.83[CEU][hapmap]
rs28719490	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890313	1.00[JPT][hapmap]
rs4779046	0.91[CEU][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4779051	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4779052	1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7178459	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72630439	0.82[EUR][1000 genomes]
rs783538	0.83[CEU][hapmap]
rs803686	0.85[ASW][hapmap];0.87[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	esv3413738	chr15:83390947-83422928	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7163840	LOC653344	cis	multi-tissue	Pritchard
rs7163840	FAM154B	cis	parietal	SCAN
rs7163840	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs7163840	RASGRF1	cis	cerebellum	SCAN
rs7163840	CPEB1	cis	Esophagus Muscularis	GTEx
rs7163840	BTBD1	cis	cerebellum	SCAN
rs7163840	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs7163840	YES1	trans	lymphoblastoid	RTeQTL
rs7163840	LOC402057	trans	multi-tissue	Pritchard
rs7163840	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs7163840	HDGFRP3	cis	lymphoblastoid	seeQTL
rs7163840	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs7163840	FLJ22795///LOC727751	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83393600-83406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:83393800-83418400	Weak transcription	Thymus	Thymus
3	chr15:83394200-83404600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:83394400-83418200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:83394400-83418400	Weak transcription	Primary B cells from cord blood	blood
6	chr15:83394600-83407200	Weak transcription	HSMMtube	muscle
7	chr15:83394800-83418400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:83395600-83407600	Weak transcription	Spleen	Spleen
9	chr15:83395800-83401000	Weak transcription	Primary T cells from cord blood	blood
10	chr15:83395800-83418200	Weak transcription	GM12878-XiMat	blood
11	chr15:83396000-83403800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr15:83396200-83401000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:83396200-83402600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:83396200-83403600	Weak transcription	Liver	Liver
15	chr15:83396200-83417800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:83396400-83401400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:83396600-83418200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:83397400-83403800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr15:83397600-83403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:83397600-83410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:83398000-83409200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:83398200-83405600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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