Variant report

Variant	rs9996382
Chromosome Location	chr4:120151012-120151013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120136237..120140737-chr4:120147652..120152174,4	MCF-7	breast:
2	chr4:120146321..120148170-chr4:120150599..120152803,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10003567	0.90[CEU][hapmap]
rs10006259	0.90[CEU][hapmap]
rs10006304	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10010696	0.83[EUR][1000 genomes]
rs10013032	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10013042	0.90[CEU][hapmap]
rs10022508	0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031033	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1011054	0.81[CEU][hapmap]
rs1033087	0.88[ASN][1000 genomes]
rs10518300	0.90[CEU][hapmap]
rs11098490	0.84[ASN][1000 genomes]
rs11098491	0.84[ASN][1000 genomes]
rs11098492	0.87[ASN][1000 genomes]
rs11098493	0.87[ASN][1000 genomes]
rs11098499	0.81[CEU][hapmap]
rs11098501	0.90[CEU][hapmap]
rs11726229	0.80[CEU][hapmap]
rs11732686	0.89[CEU][hapmap]
rs11733239	0.83[ASN][1000 genomes]
rs11931312	0.82[EUR][1000 genomes]
rs11944880	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs12186259	0.83[EUR][1000 genomes]
rs12502503	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12507565	0.90[CEU][hapmap]
rs12509054	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12511640	0.90[CEU][hapmap]
rs12513083	0.89[CEU][hapmap]
rs12513191	0.87[ASN][1000 genomes]
rs12711071	0.90[CEU][hapmap]
rs13113112	0.81[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs13114751	0.83[EUR][1000 genomes]
rs13120560	0.85[ASN][1000 genomes]
rs13123591	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13126596	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13129661	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs13136593	0.87[ASN][1000 genomes]
rs13138782	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1397608	0.83[EUR][1000 genomes]
rs1511017	0.90[CEU][hapmap]
rs1511018	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1511019	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1511025	0.90[CEU][hapmap];0.88[MEX][hapmap]
rs1546503	0.90[CEU][hapmap]
rs1551	0.82[EUR][1000 genomes]
rs17839089	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980025	0.90[CEU][hapmap]
rs1980026	0.90[CEU][hapmap]
rs2036861	0.88[ASN][1000 genomes]
rs2203039	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28452522	0.94[ASN][1000 genomes]
rs35271032	0.83[EUR][1000 genomes]
rs35916640	0.82[EUR][1000 genomes]
rs3749591	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs4145951	0.82[EUR][1000 genomes]
rs4355373	0.84[ASN][1000 genomes]
rs4833612	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833613	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs56122576	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56386062	0.83[EUR][1000 genomes]
rs6534130	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67073020	0.81[EUR][1000 genomes]
rs68128210	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815725	0.83[EUR][1000 genomes]
rs6822498	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6826823	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6832670	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837898	0.81[CEU][hapmap]
rs6838674	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6845702	0.84[ASN][1000 genomes]
rs6849889	0.81[CEU][hapmap]
rs6851130	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6851169	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs714899	0.86[CEU][hapmap]
rs7441137	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7659194	0.81[CEU][hapmap]
rs7661020	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672594	0.90[CEU][hapmap]
rs7684942	0.82[EUR][1000 genomes]
rs7685268	0.83[EUR][1000 genomes]
rs878372	0.90[CEU][hapmap]
rs907205	0.90[CEU][hapmap]
rs951570	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9884728	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991959	0.90[CEU][hapmap]
rs9993110	0.85[ASN][1000 genomes]
rs9995277	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9999724	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	esv2763386	chr4:120143861-120186968	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv966480	chr4:120144708-120160847	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9996382	USP53	cis	parietal	SCAN
rs9996382	BBS7	cis	cerebellum	SCAN
rs9996382	RP11-384K6.6	cis	Whole Blood	GTEx
rs9996382	RP11-384K6.6	cis	Artery Tibial	GTEx
rs9996382	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs9996382	C4orf3	cis	cerebellum	SCAN
rs9996382	USP53	cis	cerebellum	SCAN
rs9996382	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	lesional skin	skin_eQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:120135000-120154800	Weak transcription	Primary B cells from cord blood	blood
3	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:120135200-120155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:120135200-120155000	Weak transcription	Small Intestine	intestine
7	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:120135400-120159000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:120135600-120155000	Weak transcription	K562	blood
13	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
14	chr4:120136200-120154400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
16	chr4:120136400-120151600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:120136400-120155000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:120136400-120155000	Weak transcription	Stomach Mucosa	stomach
19	chr4:120136400-120156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:120137400-120155000	Weak transcription	Right Atrium	heart
21	chr4:120137600-120154600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr4:120138800-120155000	Weak transcription	Fetal Thymus	thymus
23	chr4:120139400-120151400	Weak transcription	HepG2	liver
24	chr4:120139400-120151600	Weak transcription	Psoas Muscle	Psoas
25	chr4:120139400-120165800	Weak transcription	Fetal Kidney	kidney
26	chr4:120139600-120151200	Weak transcription	Primary T cells from cord blood	blood
27	chr4:120139600-120151600	Weak transcription	Aorta	Aorta
28	chr4:120139600-120153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:120140000-120155000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:120140200-120154800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:120140200-120154800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:120140600-120151400	Weak transcription	Left Ventricle	heart
33	chr4:120140600-120151600	Weak transcription	Right Ventricle	heart
34	chr4:120140600-120167400	Weak transcription	Colonic Mucosa	Colon
35	chr4:120140800-120152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:120140800-120154600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:120140800-120154800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:120140800-120158800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:120141000-120151200	Weak transcription	Liver	Liver
40	chr4:120141000-120153800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:120141000-120154600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:120141000-120154600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:120141000-120154800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:120141000-120158800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
46	chr4:120141400-120151800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:120141400-120151800	Weak transcription	HUVEC	blood vessel
48	chr4:120142400-120155000	Weak transcription	Ovary	ovary
49	chr4:120143000-120151800	Weak transcription	Lung	lung
50	chr4:120143000-120155000	Weak transcription	Primary T cells fromperipheralblood	blood

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