Variant report

Variant	rs4869767
Chromosome Location	chr6:150245110-150245111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:150245071-150245121	CMK	blood:	n/a
2	chr6:150245071-150245121	AG04449	skin:	fetal
3	chr6:150245071-150245121	HCF	heart:	n/a
4	chr6:150245071-150245121	K562	blood:	n/a
5	chr6:150245071-150245121	MCF10A-Er-Src	breast:	n/a
6	chr6:150245071-150245121	HRCEpiC	kidney:	n/a
7	chr6:150245071-150245121	HEK293	kidney:	embryo
8	chr6:150245071-150245121	ProgFib	skin:	n/a
9	chr6:150245071-150245121	BE2_C	brain:	n/a
10	chr6:150245071-150245121	PrEC	prostate:	n/a
11	chr6:150245071-150245121	GM12891	blood:	n/a
12	chr6:150245071-150245121	GM12878	blood:	n/a
13	chr6:150245071-150245121	HRE	kidney:	n/a
14	chr6:150245071-150245121	NH-A	brain:	n/a
15	chr6:150245071-150245121	AG04450	lung:	fetal
16	chr6:150245071-150245121	T-47D	breast:	n/a
17	chr6:150245071-150245121	GM12892	blood:	n/a
18	chr6:150245071-150245121	NHDF-neo	bronchial:	n/a
19	chr6:150245071-150245121	Jurkat	blood:	n/a
20	chr6:150245071-150245121	HUVEC	blood vessel:	n/a
21	chr6:150245071-150245121	NB4	blood:	n/a
22	chr6:150245071-150245121	AG09309	skin:	n/a
23	chr6:150245071-150245121	NT2-D1	testis:	n/a
24	chr6:150245071-150245121	Caco-2	colon:	n/a
25	chr6:150245071-150245121	AoSMC	blood vessel:	n/a
26	chr6:150245071-150245121	HIPEpiC	eye:	n/a
27	chr6:150245071-150245121	SK-N-MC	brain:	n/a
28	chr6:150245071-150245121	HEEpiC	esophagus:	n/a
29	chr6:150245071-150245121	ovcar-3	ovarian:	n/a
30	chr6:150245071-150245121	GM06990	blood:	n/a
31	chr6:150245071-150245121	Hepatocyte	liver:	n/a
32	chr6:150245071-150245121	HMEC	breast:	n/a
33	chr6:150245071-150245121	GM19239	blood:	n/a
34	chr6:150245071-150245121	HCT-116	colon:	n/a
35	chr6:150245071-150245121	SAEC	small airway:	n/a
36	chr6:150245071-150245121	A549	lung:	n/a
37	chr6:150245071-150245121	SK-N-SH_RA	brain:	n/a
38	chr6:150245071-150245121	HCPEpiC	choroid plexus:	n/a
39	chr6:150245071-150245121	ECC-1	luminal epithelium:	n/a
40	chr6:150245071-150245121	HAEpiC	amniotic membrane:	n/a
41	chr6:150245071-150245121	HL-60	blood:	n/a
42	chr6:150245071-150245121	BJ	skin:	n/a
43	chr6:150245071-150245121	LNCaP	prostate:	n/a
44	chr6:150245071-150245121	Hela-S3	cervix:	n/a
45	chr6:150245071-150245121	RPTEC	kidney:	n/a
46	chr6:150245071-150245121	U87	brain:	n/a
47	chr6:150245071-150245121	MCF-7	breast:	n/a
48	chr6:150245071-150245121	SKMC	muscle:	n/a
49	chr6:150245071-150245121	HRPEpiC	eye:	n/a
50	chr6:150245071-150245121	IMR90	lung:	fetal

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149865589..149867401-chr6:150242514..150245357,2	MCF-7	breast:
2	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:
3	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:

No data

Variant related genes	Relation type
RAET1G	CpG island
ENSG00000164520	Chromatin interaction
ENSG00000131013	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10457852	0.94[CEU][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12204653	0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12209310	0.92[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210822	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12527391	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12528243	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1855572	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1999632	0.89[CEU][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1999633	0.83[CEU][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2342766	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3798763	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3922946	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3922947	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473864	0.92[ASN][1000 genomes]
rs4869755	0.94[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869756	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870078	0.94[CEU][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4870110	0.92[ASN][1000 genomes]
rs4870117	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4870118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5024811	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57894361	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6557165	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6912330	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914185	0.83[ASN][1000 genomes]
rs6925151	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7452592	0.84[EUR][1000 genomes]
rs7764677	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs915140	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322229	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9371228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383941	0.92[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9397070	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4869767	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs4869767	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs4869767	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4869767	LRP11	cis	cerebellum	SCAN
rs4869767	LATS1	cis	cerebellum	SCAN
rs4869767	RP11-350J20.5	cis	lung	GTEx
rs4869767	RAET1G	cis	Thyroid	GTEx
rs4869767	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs4869767	LRP11	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:150244000-150246200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:150244200-150246800	Enhancers	Spleen	Spleen
4	chr6:150244600-150245200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
5	chr6:150244600-150245200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:150244600-150245200	Bivalent Enhancer	Fetal Thymus	thymus
7	chr6:150244800-150245200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr6:150244800-150245200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr6:150244800-150245200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:150244800-150245200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:150244800-150245200	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr6:150244800-150245200	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr6:150244800-150245800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
14	chr6:150244800-150246000	Weak transcription	Esophagus	oesophagus
15	chr6:150244800-150246000	Weak transcription	Left Ventricle	heart
16	chr6:150244800-150246000	Weak transcription	NHDF-Ad	bronchial
17	chr6:150244800-150246200	Weak transcription	NHLF	lung
18	chr6:150244800-150246400	Weak transcription	Liver	Liver
19	chr6:150244800-150246400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:150244800-150246400	Weak transcription	Right Ventricle	heart
21	chr6:150244800-150246400	Weak transcription	HUVEC	blood vessel
22	chr6:150244800-150246400	Weak transcription	NHEK	skin
23	chr6:150244800-150246600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:150244800-150246600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:150244800-150246600	Weak transcription	Brain Angular Gyrus	brain
26	chr6:150244800-150246600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:150244800-150246600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr6:150244800-150246800	Weak transcription	Aorta	Aorta
29	chr6:150244800-150246800	Weak transcription	Gastric	stomach
30	chr6:150244800-150246800	Weak transcription	Lung	lung
31	chr6:150244800-150246800	Weak transcription	HSMM	muscle
32	chr6:150244800-150246800	Weak transcription	HSMMtube	muscle
33	chr6:150244800-150247000	Weak transcription	A549	lung
34	chr6:150244800-150247000	Weak transcription	Hela-S3	cervix
35	chr6:150245000-150245200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
36	chr6:150245000-150245200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
37	chr6:150245000-150245200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
38	chr6:150245000-150245200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr6:150245000-150245200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:150245000-150245600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:150245000-150246000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:150245000-150246000	Weak transcription	Adipose Nuclei	Adipose
43	chr6:150245000-150246200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:150245000-150246200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:150245000-150246200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:150245000-150246200	Weak transcription	Pancreas	Pancrea
47	chr6:150245000-150246200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:150245000-150246400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:150245000-150246400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:150245000-150246400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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