Variant report

Variant	rs3972617
Chromosome Location	chr15:78335891-78335892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78334090..78336952-chr15:78350670..78353482,2	MCF-7	breast:
2	chr15:78329401..78332301-chr15:78334192..78337171,4	K562	blood:
3	chr15:78335660..78338576-chr15:78374188..78376169,2	MCF-7	breast:
4	chr15:78330789..78332749-chr15:78335329..78337205,2	K562	blood:

Variant related genes	Relation type
ENSG00000221476	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1053506	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11633329	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633569	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636889	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854102	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12595595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898535	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900731	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901492	1.00[ASN][1000 genomes]
rs12913206	1.00[ASN][1000 genomes]
rs12915731	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915847	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837911	1.00[ASN][1000 genomes]
rs1837912	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015951	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867984	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4243073	0.82[AFR][1000 genomes]
rs4316722	1.00[ASN][1000 genomes]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886985	1.00[ASN][1000 genomes]
rs4886986	1.00[ASN][1000 genomes]
rs4886987	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886991	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886993	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886997	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886998	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887001	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887003	1.00[ASN][1000 genomes]
rs4887004	1.00[ASN][1000 genomes]
rs61732053	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163997	1.00[ASN][1000 genomes]
rs7169381	0.81[AMR][1000 genomes]
rs7169882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170286	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170452	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175192	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025423	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033216	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894295	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894296	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894302	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788640	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920180	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:78321200-78343800	Weak transcription	NHEK	skin
11	chr15:78322200-78336600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:78322200-78341000	Weak transcription	Brain Germinal Matrix	brain
13	chr15:78322400-78336600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:78325600-78337800	Genic enhancers	Fetal Thymus	thymus
15	chr15:78327400-78339600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:78327800-78342000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr15:78328000-78336600	Weak transcription	Fetal Brain Female	brain
19	chr15:78328000-78336800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:78328000-78341800	Weak transcription	Fetal Brain Male	brain
21	chr15:78328400-78339000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:78328400-78342200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:78328600-78336400	Weak transcription	NH-A	brain
24	chr15:78328600-78342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:78329000-78342400	Weak transcription	Fetal Heart	heart
26	chr15:78329400-78336200	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:78329600-78339000	Weak transcription	Stomach Mucosa	stomach
28	chr15:78330600-78342800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:78331000-78336200	Strong transcription	Fetal Stomach	stomach
30	chr15:78331000-78336600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:78331000-78337000	Strong transcription	HSMM	muscle
32	chr15:78331000-78339200	Weak transcription	Brain Angular Gyrus	brain
33	chr15:78331200-78336600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:78331200-78344400	Weak transcription	Psoas Muscle	Psoas
35	chr15:78331400-78336800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr15:78331400-78339600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:78331400-78348600	Weak transcription	A549	lung
38	chr15:78331600-78337400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:78331600-78339000	Weak transcription	Right Ventricle	heart
40	chr15:78331600-78339800	Weak transcription	HUVEC	blood vessel
41	chr15:78331600-78348600	Weak transcription	K562	blood
42	chr15:78332000-78336600	Strong transcription	Fetal Intestine Large	intestine
43	chr15:78332000-78336600	Strong transcription	Placenta	Placenta
44	chr15:78332000-78336800	Strong transcription	Fetal Intestine Small	intestine
45	chr15:78332000-78337000	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:78332000-78342200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:78332200-78336400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr15:78332200-78337000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:78332400-78336600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:78332600-78336600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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