Variant report

Variant	rs1632949
Chromosome Location	chr6:29793724-29793725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr6:29793627-29793929	H1-hESC	embryonic stem cell:	n/a	chr6:29793830-29793841
2	USF1	chr6:29793518-29794103	HCT-116	colon:	n/a	chr6:29793830-29793841
3	USF1	chr6:29793607-29793968	H1-hESC	embryonic stem cell:	n/a	chr6:29793830-29793841

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29793709-29793759	HEEpiC	esophagus:	n/a
2	chr6:29793709-29793759	NHDF-neo	bronchial:	n/a
3	chr6:29793709-29793759	GM12878	blood:	n/a
4	chr6:29793709-29793759	CMK	blood:	n/a
5	chr6:29793709-29793759	HNPCEpiC	eye:	n/a
6	chr6:29793709-29793759	Hepatocyte	liver:	n/a
7	chr6:29793709-29793759	U87	brain:	n/a
8	chr6:29793709-29793759	IMR90	lung:	fetal
9	chr6:29793709-29793759	PFSK-1	brain:	n/a
10	chr6:29793709-29793759	ovcar-3	ovarian:	n/a
11	chr6:29793709-29793759	ProgFib	skin:	n/a
12	chr6:29793709-29793759	GM12892	blood:	n/a
13	chr6:29793709-29793759	HCM	heart:	n/a
14	chr6:29793709-29793759	PANC-1	pancreas:	n/a
15	chr6:29793709-29793759	ECC-1	luminal epithelium:	n/a
16	chr6:29793709-29793759	HCF	heart:	n/a
17	chr6:29793709-29793759	NT2-D1	testis:	n/a
18	chr6:29793709-29793759	MCF10A-Er-Src	breast:	n/a
19	chr6:29793709-29793759	HAEpiC	amniotic membrane:	n/a
20	chr6:29793709-29793759	SAEC	small airway:	n/a
21	chr6:29793709-29793759	HCPEpiC	choroid plexus:	n/a
22	chr6:29793709-29793759	HRCEpiC	kidney:	n/a
23	chr6:29793709-29793759	K562	blood:	n/a
24	chr6:29793709-29793759	GM19239	blood:	n/a
25	chr6:29793709-29793759	NH-A	brain:	n/a
26	chr6:29793709-29793759	HIPEpiC	eye:	n/a
27	chr6:29793709-29793759	Hela-S3	cervix:	n/a
28	chr6:29793709-29793759	HRPEpiC	eye:	n/a
29	chr6:29793709-29793759	NHBE	bronchial:	n/a
30	chr6:29793709-29793759	MCF-7	breast:	n/a
31	chr6:29793709-29793759	SK-N-SH	brain:	n/a
32	chr6:29793709-29793759	SK-N-SH_RA	brain:	n/a
33	chr6:29793709-29793759	Jurkat	blood:	n/a
34	chr6:29793709-29793759	GM12891	blood:	n/a
35	chr6:29793709-29793759	LNCaP	prostate:	n/a
36	chr6:29793709-29793759	NB4	blood:	n/a
37	chr6:29793709-29793759	AG10803	skin:	n/a
38	chr6:29793709-29793759	BE2_C	brain:	n/a
39	chr6:29793709-29793759	SK-N-MC	brain:	n/a
40	chr6:29793709-29793759	T-47D	breast:	n/a
41	chr6:29793709-29793759	A549	lung:	n/a
42	chr6:29793709-29793759	HUVEC	blood vessel:	n/a
43	chr6:29793709-29793759	AG04450	lung:	fetal
44	chr6:29793709-29793759	AG04449	skin:	fetal
45	chr6:29793709-29793759	H1-hESC	embryonic stem cell:	embryo
46	chr6:29793709-29793759	Caco-2	colon:	n/a
47	chr6:29793709-29793759	GM06990	blood:	n/a
48	chr6:29793709-29793759	SKMC	muscle:	n/a
49	chr6:29793709-29793759	PrEC	prostate:	n/a
50	chr6:29793709-29793759	HEK293	kidney:	embryo

No data

Variant related genes	Relation type
HLA-G	TF binding region
HLA-G	CpG island

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1077432	0.87[AFR][1000 genomes]
rs1077433	0.88[AFR][1000 genomes]
rs1079599	0.88[AFR][1000 genomes]
rs1111673	0.88[AFR][1000 genomes]
rs1155143	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1318083	0.88[AFR][1000 genomes]
rs1610673	0.86[AFR][1000 genomes]
rs1610675	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610696	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610700	0.86[AFR][1000 genomes]
rs1610704	0.80[AFR][1000 genomes]
rs1611139	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611142	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1611143	0.87[AFR][1000 genomes]
rs1611158	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1611159	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611162	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611166	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611184	0.86[AFR][1000 genomes]
rs1619379	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1620173	0.88[AFR][1000 genomes]
rs1632950	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633039	0.89[AFR][1000 genomes]
rs1633047	0.93[AFR][1000 genomes]
rs1633078	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1633108	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736942	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1736948	0.93[AFR][1000 genomes]
rs1736950	0.93[AFR][1000 genomes]
rs1736955	0.88[AFR][1000 genomes]
rs1736958	0.88[AFR][1000 genomes]
rs1736959	0.88[AFR][1000 genomes]
rs2735024	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6941241	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs753544	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	esv3423001	chr6:29733216-29878601	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	esv3475027	chr6:29733297-29922699	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	esv3475028	chr6:29733297-29922699	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	esv3420260	chr6:29734457-29835593	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	esv3330285	chr6:29736281-29881328	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	esv3396224	chr6:29754243-29888093	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
15	nsv965702	chr6:29758408-29798943	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
17	esv3426050	chr6:29761594-29918407	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
18	esv3431350	chr6:29765473-29922767	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
19	esv3354193	chr6:29773857-29867902	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
20	esv3451016	chr6:29774115-29929436	Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
21	esv3369144	chr6:29775824-29872385	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
22	esv3500392	chr6:29777854-29871802	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
23	esv3500393	chr6:29777854-29871802	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	esv3384912	chr6:29778488-29872579	ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	esv3431922	chr6:29779132-29873171	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
26	esv3338581	chr6:29780045-29890754	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
27	esv17468	chr6:29782014-29923275	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
28	esv3411103	chr6:29783090-29930409	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
29	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
30	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
31	esv20324	chr6:29793378-29832922	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1632949	HIST1H2BL	cis	parietal	SCAN
rs1632949	HCG4	cis	uninvolved skin	skin_eQTL
rs1632949	HCG4	cis	lesional skin	skin_eQTL
rs1632949	HIST1H2AM	cis	cerebellum	SCAN
rs1632949	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs1632949	GPX6	cis	parietal	SCAN
rs1632949	HIST1H2AM	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29793400-29794800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:29793400-29795600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:29793400-29795600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:29793600-29793800	Enhancers	Lung	lung
5	chr6:29793600-29794600	Enhancers	NHEK	skin
6	chr6:29793600-29794800	Enhancers	HMEC	breast
7	chr6:29793600-29795400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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