Variant report

Variant	rs6533197
Chromosome Location	chr4:106387894-106387895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106160813..106162575-chr4:106387724..106390093,2	K562	blood:
2	chr4:106366716..106368636-chr4:106386023..106388059,2	K562	blood:
3	chr4:106354166..106355972-chr4:106386471..106389222,2	K562	blood:
4	chr4:106385665..106390860-chr4:106392810..106395271,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10007134	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10020998	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1125254	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934602	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11934709	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2023840	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2046880	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298732	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2636727	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2636747	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2713826	0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2866883	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35775499	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3864225	0.97[ASN][1000 genomes]
rs4235414	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699176	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699178	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533196	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533198	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533199	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533201	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6816997	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836448	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs763289	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678401	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7691192	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8180199	0.97[ASN][1000 genomes]
rs981136	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9990819	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9999896	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
2	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
4	chr4:106348000-106388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
6	chr4:106355400-106393200	Weak transcription	Esophagus	oesophagus
7	chr4:106357200-106392600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:106357600-106392200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:106362200-106392600	Weak transcription	A549	lung
10	chr4:106363800-106390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:106364600-106392000	Weak transcription	Brain Anterior Caudate	brain
12	chr4:106364600-106392600	Weak transcription	Fetal Kidney	kidney
13	chr4:106366000-106392400	Weak transcription	Osteobl	bone
14	chr4:106366000-106392600	Weak transcription	Psoas Muscle	Psoas
15	chr4:106366600-106392200	Weak transcription	Liver	Liver
16	chr4:106366600-106392200	Weak transcription	HepG2	liver
17	chr4:106366600-106392600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:106366800-106393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:106368200-106392000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:106369400-106388800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:106369600-106388000	Weak transcription	Hela-S3	cervix
22	chr4:106370000-106392600	Weak transcription	HUVEC	blood vessel
23	chr4:106373200-106392600	Weak transcription	NH-A	brain
24	chr4:106373400-106390600	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:106373400-106392200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:106374000-106392400	Weak transcription	NHDF-Ad	bronchial
27	chr4:106374000-106393000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:106374600-106392400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:106374600-106392600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:106375000-106391400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:106375400-106392600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:106375400-106393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:106375400-106393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:106376800-106392600	Weak transcription	Fetal Lung	lung
35	chr4:106377000-106393000	Weak transcription	Right Atrium	heart
36	chr4:106377000-106393200	Weak transcription	Pancreas	Pancrea
37	chr4:106377000-106394000	Weak transcription	Gastric	stomach
38	chr4:106377800-106388600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:106377800-106388800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:106378000-106392200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:106378000-106392200	Weak transcription	HMEC	breast
42	chr4:106378000-106392400	Weak transcription	HSMM	muscle
43	chr4:106378000-106393000	Weak transcription	HSMMtube	muscle
44	chr4:106379200-106392200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:106379200-106392600	Weak transcription	Aorta	Aorta
46	chr4:106379600-106392200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:106381200-106394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:106381400-106390200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:106381600-106392600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:106382000-106392400	Weak transcription	Brain Substantia Nigra	brain

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