Variant report

Variant	rs2867985
Chromosome Location	chr15:78363775-78363776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78362996..78365897-chr15:78366671..78369435,4	MCF-7	breast:
2	chr15:78354817..78358592-chr15:78361208..78364275,3	MCF-7	breast:
3	chr15:78362119..78363904-chr15:78366538..78368474,2	MCF-7	breast:
4	chr15:78354448..78356062-chr15:78363127..78365544,2	K562	blood:

Variant related genes	Relation type
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1004855	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10519181	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs11072716	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11631578	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs11634607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs11852768	0.96[ASN][1000 genomes]
rs12148365	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442213	0.83[CHB][hapmap]
rs12591418	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs12594823	0.91[CHB][hapmap];0.97[CHD][hapmap]
rs12899061	0.95[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs12907701	0.93[ASN][1000 genomes]
rs12907814	0.95[ASN][1000 genomes]
rs12911332	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs12916362	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs1348257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs1837913	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap]
rs2028546	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2044099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs2903702	0.98[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs4395040	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs4886553	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs4886554	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs4886555	0.99[ASN][1000 genomes]
rs4886994	0.85[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap]
rs4886996	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs4886999	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs56317829	0.97[ASN][1000 genomes]
rs57220134	0.98[ASN][1000 genomes]
rs58578288	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62011511	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166819	0.96[ASN][1000 genomes]
rs7170746	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs7173128	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs7181594	0.96[ASN][1000 genomes]
rs8029562	0.90[ASN][1000 genomes]
rs8030873	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9047	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2867985	MORF4L1	cis	parietal	SCAN
rs2867985	ISL2	cis	parietal	SCAN
rs2867985	CLK3	cis	cerebellum	SCAN
rs2867985	HEXA	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78347400-78367800	Enhancers	Placenta	Placenta
2	chr15:78354200-78366400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:78354600-78365400	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr15:78354600-78366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:78355200-78364000	Enhancers	Dnd41	blood
6	chr15:78355600-78365400	Enhancers	Small Intestine	intestine
7	chr15:78355800-78364000	Enhancers	Fetal Muscle Leg	muscle
8	chr15:78356000-78363800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:78357400-78364400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:78357400-78365000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr15:78357600-78365200	Enhancers	Lung	lung
12	chr15:78358400-78366000	Enhancers	HepG2	liver
13	chr15:78358800-78367800	Weak transcription	HMEC	breast
14	chr15:78360200-78363800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:78361200-78364400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:78361200-78364600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:78361200-78364600	Enhancers	NHDF-Ad	bronchial
18	chr15:78361200-78364800	Enhancers	Osteobl	bone
19	chr15:78361200-78365200	Weak transcription	Fetal Brain Male	brain
20	chr15:78361400-78364200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:78361400-78364600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:78361400-78364800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:78361400-78364800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:78361400-78367800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:78361400-78368000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:78361400-78368000	Weak transcription	Fetal Heart	heart
27	chr15:78361400-78368200	Weak transcription	Brain Germinal Matrix	brain
28	chr15:78361600-78364000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:78361600-78364200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:78361600-78364400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:78361600-78364600	Weak transcription	Aorta	Aorta
32	chr15:78361600-78364800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr15:78361600-78364800	Weak transcription	Fetal Brain Female	brain
34	chr15:78361600-78365400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr15:78361600-78369200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:78361800-78364200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:78361800-78364400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:78361800-78364400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:78362000-78364200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:78362000-78365000	Enhancers	Primary B cells from cord blood	blood
41	chr15:78362000-78366000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:78362400-78364400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr15:78362600-78364000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr15:78362600-78364400	Weak transcription	Fetal Kidney	kidney
45	chr15:78362600-78364800	Enhancers	Duodenum Mucosa	Duodenum
46	chr15:78362600-78365600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:78362600-78365600	Enhancers	Thymus	Thymus
48	chr15:78362800-78363800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:78362800-78363800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:78362800-78363800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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