Variant report

Variant	rs17394732
Chromosome Location	chr15:77835657-77835658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77399766..77400631-chr15:77835398..77836258,2	K562	blood:
2	chr15:77835401..77836400-chr15:77925681..77926470,4	K562	blood:
3	chr15:77835384..77837203-chr15:77911255..77913813,2	MCF-7	breast:
4	chr15:77793530..77795240-chr15:77834025..77836291,2	MCF-7	breast:
5	chr15:77835406..77836055-chr15:77951749..77952721,2	K562	blood:
6	chr15:77835344..77836277-chr15:77947161..77947947,2	K562	blood:
7	chr15:77824813..77828626-chr15:77832957..77835709,3	K562	blood:
8	chr15:77829651..77831982-chr15:77834371..77837022,2	MCF-7	breast:
9	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
10	chr15:77316409..77317242-chr15:77835418..77836097,2	MCF-7	breast:
11	chr15:77320665..77321535-chr15:77835341..77836068,2	K562	blood:
12	chr15:77316331..77317283-chr15:77835334..77836400,5	K562	blood:
13	chr15:77833246..77835948-chr15:77846373..77848114,2	MCF-7	breast:
14	chr15:77788121..77789886-chr15:77835389..77836306,7	MCF-7	breast:
15	chr15:77795040..77797177-chr15:77834449..77837320,2	MCF-7	breast:
16	chr15:77833855..77835939-chr15:77840027..77842265,2	K562	blood:
17	chr15:77835455..77836319-chr15:77923426..77923976,2	MCF-7	breast:
18	chr15:77478337..77479628-chr15:77835376..77836422,12	MCF-7	breast:
19	chr15:77789332..77790391-chr15:77834947..77835831,3	MCF-7	breast:
20	chr15:77835652..77836578-chr15:77876310..77876975,3	MCF-7	breast:
21	chr15:77795420..77798597-chr15:77834386..77837370,5	MCF-7	breast:
22	chr15:77827126..77831240-chr15:77834209..77836612,4	K562	blood:
23	chr15:77835482..77836422-chr15:78167231..78168063,2	K562	blood:
24	chr15:77787983..77789966-chr15:77835290..77836892,2	MCF-7	breast:
25	chr15:77411217..77412383-chr15:77835511..77836330,5	MCF-7	breast:
26	chr15:77835573..77836399-chr15:77908014..77909056,3	MCF-7	breast:
27	chr15:77399499..77401311-chr15:77835017..77836203,9	MCF-7	breast:
28	chr15:77478458..77479486-chr15:77835010..77836461,5	MCF-7	breast:
29	chr15:77793037..77794591-chr15:77835207..77836439,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140368	Chromatin interaction
ENSG00000259281	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11630540	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11630557	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630916	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630926	0.90[ASN][1000 genomes]
rs11631274	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634174	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs11635226	0.80[EUR][1000 genomes]
rs11635567	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11635606	0.90[ASN][1000 genomes]
rs11636231	0.80[EUR][1000 genomes]
rs11636529	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11637932	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11639293	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs12898370	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs12898656	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs12899390	0.93[ASN][1000 genomes]
rs12901100	0.92[ASN][1000 genomes]
rs12901471	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12901732	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12901765	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12901998	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12902072	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12902379	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902698	0.82[CEU][hapmap]
rs12902896	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs12902898	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12902925	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902948	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12904200	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12904208	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12904212	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904254	0.86[JPT][hapmap]
rs12904348	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904533	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12904584	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904709	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12905044	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12905318	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12909292	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12909645	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12909808	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910512	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910513	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910594	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910951	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs12910975	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911649	0.88[CEU][hapmap]
rs12911854	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911963	0.88[CEU][hapmap]
rs12912386	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12913005	0.80[EUR][1000 genomes]
rs12914098	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12914932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12915057	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12915548	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916515	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916642	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916682	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs12916822	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916833	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916973	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs12917044	1.00[CEU][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12917175	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917314	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917431	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34020536	0.90[ASN][1000 genomes]
rs34075648	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34607443	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34829483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35577135	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35657172	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55883527	0.80[EUR][1000 genomes]
rs59418918	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62009067	0.90[ASN][1000 genomes]
rs62009069	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62009071	0.88[ASN][1000 genomes]
rs62009087	0.99[ASN][1000 genomes]
rs7176307	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176875	0.97[ASN][1000 genomes]
rs7180732	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181283	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs8025968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8032405	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033067	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033654	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040318	0.88[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs8040702	0.88[CEU][hapmap]
rs8041398	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8041520	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042307	0.88[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS 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	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17394732	ABCB8	trans	parietal	SCAN
rs17394732	HMG20A	cis	parietal	SCAN
rs17394732	SGK269	cis	parietal	SCAN
rs17394732	STRA6	cis	cerebellum	SCAN
rs17394732	HMG20A	cis	cerebellum	SCAN
rs17394732	RP11-307C19.1	cis	Heart Left Ventricle	GTEx
rs17394732	C15orf5	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
2	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77832800-77836000	Enhancers	NHDF-Ad	bronchial
4	chr15:77833000-77836600	Enhancers	Fetal Brain Male	brain
5	chr15:77833200-77836200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:77833800-77843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:77834000-77841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:77834200-77840800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:77834800-77836200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:77834800-77837200	Enhancers	Gastric	stomach
11	chr15:77835000-77835800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:77835000-77836200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:77835000-77836200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr15:77835000-77836200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:77835000-77836200	Enhancers	Lung	lung
16	chr15:77835000-77836200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr15:77835000-77836600	Enhancers	Fetal Heart	heart
18	chr15:77835200-77835800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:77835200-77835800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:77835200-77835800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr15:77835200-77835800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:77835200-77835800	Enhancers	Aorta	Aorta
23	chr15:77835200-77835800	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr15:77835200-77835800	Flanking Active TSS	Colonic Mucosa	Colon
25	chr15:77835200-77835800	Flanking Active TSS	HSMMtube	muscle
26	chr15:77835200-77836000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr15:77835200-77836000	Flanking Active TSS	Fetal Muscle Leg	muscle
28	chr15:77835200-77836200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr15:77835200-77836200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr15:77835200-77836200	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr15:77835200-77836200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
32	chr15:77835200-77836200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr15:77835200-77836200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr15:77835200-77836200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr15:77835200-77836200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:77835200-77836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:77835200-77836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:77835200-77836200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr15:77835200-77836200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr15:77835200-77836200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr15:77835200-77836200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr15:77835200-77836200	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr15:77835200-77836200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr15:77835200-77836200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr15:77835200-77836200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr15:77835200-77836200	Flanking Active TSS	GM12878-XiMat	blood
47	chr15:77835200-77836200	Flanking Active TSS	HMEC	breast
48	chr15:77835200-77836200	Flanking Active TSS	HSMM	muscle
49	chr15:77835200-77836200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr15:77835400-77835800	Enhancers	H1 Cell Line	embryonic stem cell

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