Variant report

Variant	rs6780005
Chromosome Location	chr3:52636615-52636616
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52635882..52639721-chr3:52640182..52642371,3	K562	blood:
2	chr3:52635643..52638367-chr3:52718395..52720556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10510759	1.00[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11510435	0.87[EUR][1000 genomes]
rs12107484	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17052357	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17052404	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1987234	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35911561	0.95[YRI][hapmap]
rs35920544	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4532127	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs56134416	0.87[EUR][1000 genomes]
rs56156188	0.87[EUR][1000 genomes]
rs56259931	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs56276589	0.87[EUR][1000 genomes]
rs56665533	0.87[EUR][1000 genomes]
rs57008939	0.87[EUR][1000 genomes]
rs57246324	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs57319306	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57560655	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57757646	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57789542	0.87[EUR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs57946083	0.87[EUR][1000 genomes]
rs58100002	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58409398	0.87[EUR][1000 genomes]
rs58528592	0.87[EUR][1000 genomes]
rs58564212	0.87[EUR][1000 genomes]
rs58725214	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58924550	0.81[AFR][1000 genomes]
rs59638016	0.87[EUR][1000 genomes]
rs59869286	0.87[EUR][1000 genomes]
rs60040519	0.87[EUR][1000 genomes]
rs60058353	0.87[EUR][1000 genomes]
rs60256157	0.87[EUR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs60415551	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60611300	0.85[AFR][1000 genomes]
rs60682984	0.85[AFR][1000 genomes]
rs60770874	0.87[EUR][1000 genomes]
rs60823713	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60830326	0.87[EUR][1000 genomes]
rs60916588	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61220667	0.87[EUR][1000 genomes]
rs61538294	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6445536	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6762788	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6769720	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6780397	0.87[EUR][1000 genomes]
rs72947535	0.81[AFR][1000 genomes]
rs72947580	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947589	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72950424	0.87[EUR][1000 genomes]
rs72950430	0.81[AFR][1000 genomes]
rs72950432	0.87[EUR][1000 genomes]
rs72950437	0.87[EUR][1000 genomes]
rs72960212	0.87[EUR][1000 genomes]
rs72960237	0.87[EUR][1000 genomes]
rs72960240	0.87[EUR][1000 genomes]
rs72960260	0.87[EUR][1000 genomes]
rs72960274	0.87[EUR][1000 genomes]
rs72960281	0.87[EUR][1000 genomes]
rs72960285	0.87[EUR][1000 genomes]
rs72965177	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73839126	0.87[EUR][1000 genomes]
rs73839129	0.87[EUR][1000 genomes]
rs7645785	0.87[EUR][1000 genomes]
rs764636	0.87[EUR][1000 genomes]
rs7647992	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7648016	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs934839	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52591000-52688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:52627800-52640600	Weak transcription	Fetal Heart	heart
5	chr3:52628600-52640200	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr3:52630800-52638600	Strong transcription	Osteobl	bone
7	chr3:52631600-52640600	Weak transcription	Stomach Mucosa	stomach
8	chr3:52632000-52638600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:52632200-52640400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:52632400-52637200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:52633000-52636800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr3:52633000-52637200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52633800-52637400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52633800-52640400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:52634000-52636800	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr3:52634000-52636800	ZNF genes & repeats	Fetal Brain Female	brain
17	chr3:52634000-52636800	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr3:52634000-52637000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:52634000-52637400	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr3:52634000-52637400	ZNF genes & repeats	GM12878-XiMat	blood
21	chr3:52634200-52636800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:52634200-52637200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:52634200-52637400	ZNF genes & repeats	Primary T cells from cord blood	blood
24	chr3:52634200-52637600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:52634200-52638000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:52634200-52640800	Strong transcription	HUVEC	blood vessel
27	chr3:52634200-52647800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:52634400-52636800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr3:52634400-52638200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:52634600-52636800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
31	chr3:52634600-52636800	ZNF genes & repeats	Thymus	Thymus
32	chr3:52634600-52637400	Strong transcription	Brain Substantia Nigra	brain
33	chr3:52634600-52638200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:52634600-52638400	Strong transcription	Liver	Liver
35	chr3:52634600-52640600	Strong transcription	Left Ventricle	heart
36	chr3:52634800-52636800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr3:52634800-52636800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:52634800-52637200	Strong transcription	A549	lung
39	chr3:52634800-52637400	Strong transcription	Small Intestine	intestine
40	chr3:52634800-52637600	Strong transcription	Rectal Smooth Muscle	rectum
41	chr3:52634800-52637600	Strong transcription	HepG2	liver
42	chr3:52634800-52638200	Strong transcription	NHDF-Ad	bronchial
43	chr3:52634800-52640800	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:52634800-52654400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:52634800-52654400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:52634800-52686000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:52635000-52636800	Strong transcription	Colon Smooth Muscle	Colon
48	chr3:52635000-52636800	Strong transcription	NHEK	skin
49	chr3:52635000-52637000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:52635000-52637400	Strong transcription	Brain Inferior Temporal Lobe	brain

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