Variant report

Variant	rs883627
Chromosome Location	chr15:77797723-77797724
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77797488..77799735-chr15:77817665..77820663,3	MCF-7	breast:
2	chr15:77786574..77788334-chr15:77795705..77797965,2	MCF-7	breast:
3	chr15:77795830..77799057-chr15:77830706..77834217,3	MCF-7	breast:
4	chr15:77795420..77798597-chr15:77834386..77837370,5	MCF-7	breast:
5	chr15:77797715..77799505-chr15:77800913..77803118,3	MCF-7	breast:
6	chr15:77789312..77792548-chr15:77795862..77798378,3	K562	blood:

Variant related genes	Relation type
ENSG00000259362	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10162778	0.86[AMR][1000 genomes]
rs11856084	0.94[JPT][hapmap]
rs12324016	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12324211	0.96[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12324795	0.83[JPT][hapmap]
rs12912084	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1493699	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16968799	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17385296	0.83[JPT][hapmap]
rs17471252	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17471480	1.00[JPT][hapmap]
rs17471697	0.94[JPT][hapmap]
rs2172587	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2307141	0.94[JPT][hapmap]
rs2864840	0.83[JPT][hapmap]
rs35651077	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3784788	0.94[JPT][hapmap]
rs4886863	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62007297	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62010566	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74026925	0.89[ASN][1000 genomes]
rs907398	0.94[JPT][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	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs883627	HMG20A	cis	parietal	SCAN
rs883627	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs883627	PSTPIP1	cis	multi-tissue	Pritchard
rs883627	CYP1A2	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77777600-77798600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:77786200-77800000	Weak transcription	Thymus	Thymus
3	chr15:77786400-77799600	Weak transcription	Primary B cells from cord blood	blood
4	chr15:77786400-77803800	Weak transcription	Primary T cells from cord blood	blood
5	chr15:77789800-77798600	Weak transcription	Gastric	stomach
6	chr15:77789800-77799600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:77789800-77801000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:77790200-77799200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr15:77790600-77799200	Weak transcription	GM12878-XiMat	blood
10	chr15:77791000-77797800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:77791000-77798600	Weak transcription	HSMM	muscle
12	chr15:77791000-77798800	Weak transcription	Fetal Intestine Large	intestine
13	chr15:77791600-77798600	Weak transcription	Fetal Kidney	kidney
14	chr15:77791600-77798800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:77791600-77798800	Weak transcription	Osteobl	bone
16	chr15:77791600-77799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:77791800-77798200	Weak transcription	Fetal Thymus	thymus
18	chr15:77792000-77798800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:77792000-77799200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:77793800-77798000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:77793800-77798600	Weak transcription	NHDF-Ad	bronchial
22	chr15:77794000-77798600	Weak transcription	NHLF	lung
23	chr15:77794200-77798800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:77794200-77799000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:77794200-77799000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:77794200-77800000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:77794800-77797800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:77794800-77799400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr15:77794800-77799800	Enhancers	HepG2	liver
30	chr15:77794800-77800600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:77795000-77798200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:77795000-77799000	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:77795400-77797800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:77795400-77799600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr15:77795400-77803000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:77795600-77800800	Enhancers	Brain Germinal Matrix	brain
37	chr15:77795800-77797800	Enhancers	Fetal Muscle Leg	muscle
38	chr15:77795800-77798000	Enhancers	Fetal Muscle Trunk	muscle
39	chr15:77795800-77798600	Enhancers	Brain Cingulate Gyrus	brain
40	chr15:77795800-77800000	Enhancers	Brain Angular Gyrus	brain
41	chr15:77795800-77800000	Enhancers	Brain Substantia Nigra	brain
42	chr15:77795800-77800400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:77795800-77801400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:77795800-77801600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr15:77796000-77797800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr15:77796000-77801800	Enhancers	Fetal Lung	lung
47	chr15:77796200-77798800	Enhancers	Brain Hippocampus Middle	brain
48	chr15:77796200-77800600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:77796400-77797800	Enhancers	Duodenum Mucosa	Duodenum
50	chr15:77796400-77801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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