Variant report

Variant	rs11732511
Chromosome Location	chr4:76425778-76425779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76425741..76429884-chr4:76437670..76440920,5	MCF-7	breast:
2	chr4:76420497..76422499-chr4:76425693..76428176,2	K562	blood:
3	chr4:76420497..76422947-chr4:76425693..76428176,3	K562	blood:
4	chr4:76423980..76426785-chr4:76427353..76430216,3	K562	blood:

Variant related genes	Relation type
ENSG00000174796	Chromatin interaction
ENSG00000163743	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10009558	0.83[YRI][hapmap]
rs10518140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721925	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11722278	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11727806	0.97[EUR][1000 genomes]
rs11729106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644911	0.82[ASN][1000 genomes]
rs12648028	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12648354	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1351094	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1904104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126854	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2306177	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867919	0.83[ASN][1000 genomes]
rs2903701	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57275697	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6836107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845472	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6845588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847297	0.84[ASN][1000 genomes]
rs6851699	0.84[ASN][1000 genomes]
rs7673610	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7683530	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs9307834	0.81[YRI][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers 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	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11732511	RCHY1	Cis_1M	lymphoblastoid	RTeQTL
rs11732511	THAP6	cis	multi-tissue	Pritchard
rs11732511	THAP6	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
3	chr4:76395800-76437000	Weak transcription	Lung	lung
4	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
5	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
6	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
11	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
12	chr4:76402200-76425800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr4:76402400-76425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:76403800-76433600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:76405600-76434400	Weak transcription	Fetal Heart	heart
16	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
19	chr4:76409400-76425800	Strong transcription	Fetal Thymus	thymus
20	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:76411400-76435400	Weak transcription	Small Intestine	intestine
22	chr4:76414600-76427000	Weak transcription	Fetal Stomach	stomach
23	chr4:76414600-76429400	Weak transcription	HSMMtube	muscle
24	chr4:76415200-76428200	Weak transcription	A549	lung
25	chr4:76415400-76430200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:76415400-76435600	Weak transcription	Brain Substantia Nigra	brain
27	chr4:76415400-76436400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:76415800-76430200	Weak transcription	Colonic Mucosa	Colon
29	chr4:76416000-76429400	Weak transcription	Left Ventricle	heart
30	chr4:76416600-76426600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:76416600-76436200	Weak transcription	Brain Anterior Caudate	brain
32	chr4:76416600-76437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:76417600-76436800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr4:76418000-76428400	Weak transcription	NH-A	brain
35	chr4:76418400-76427800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:76419000-76426000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr4:76419600-76429400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:76421200-76433600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:76421400-76437000	Weak transcription	Stomach Mucosa	stomach
40	chr4:76421800-76427800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:76422000-76426400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:76422000-76428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:76422400-76433800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr4:76422400-76434800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:76422600-76432600	Weak transcription	Colon Smooth Muscle	Colon
46	chr4:76422800-76426800	Weak transcription	HUVEC	blood vessel
47	chr4:76423000-76429000	Weak transcription	K562	blood
48	chr4:76423000-76431400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:76423000-76434400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:76423400-76426400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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