Variant report

Variant	rs9258405
Chromosome Location	chr6:29762054-29762055
allele	C/T
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:1)
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	chr6:29762010-29762060	GM06990	blood:	n/a
2	chr6:29762010-29762060	HL-60	blood:	n/a
3	chr6:29762010-29762060	GM12878	blood:	n/a
4	chr6:29762010-29762060	SK-N-SH_RA	brain:	n/a
5	chr6:29762010-29762060	ovcar-3	ovarian:	n/a
6	chr6:29762010-29762060	AG09309	skin:	n/a
7	chr6:29762010-29762060	PANC-1	pancreas:	n/a
8	chr6:29762010-29762060	SK-N-MC	brain:	n/a
9	chr6:29762010-29762060	AG10803	skin:	n/a
10	chr6:29762010-29762060	HCT-116	colon:	n/a
11	chr6:29762010-29762060	NB4	blood:	n/a
12	chr6:29762010-29762060	AG09319	gingival:	n/a
13	chr6:29762010-29762060	PrEC	prostate:	n/a
14	chr6:29762010-29762060	RPTEC	kidney:	n/a
15	chr6:29762010-29762060	MCF10A-Er-Src	breast:	n/a
16	chr6:29762010-29762060	H1-hESC	embryonic stem cell:	embryo
17	chr6:29762010-29762060	HEK293	kidney:	embryo
18	chr6:29762010-29762060	GM12892	blood:	n/a
19	chr6:29762010-29762060	HEEpiC	esophagus:	n/a
20	chr6:29762010-29762060	HAEpiC	amniotic membrane:	n/a
21	chr6:29762010-29762060	CMK	blood:	n/a
22	chr6:29762010-29762060	NHBE	bronchial:	n/a
23	chr6:29762010-29762060	Caco-2	colon:	n/a
24	chr6:29762010-29762060	BE2_C	brain:	n/a
25	chr6:29762010-29762060	HMEC	breast:	n/a
26	chr6:29762010-29762060	HepG2	liver:	n/a
27	chr6:29762010-29762060	SK-N-SH	brain:	n/a
28	chr6:29762010-29762060	AG04449	skin:	fetal
29	chr6:29762010-29762060	A549	lung:	n/a
30	chr6:29762010-29762060	HCPEpiC	choroid plexus:	n/a
31	chr6:29762010-29762060	SKMC	muscle:	n/a
32	chr6:29762010-29762060	GM12891	blood:	n/a
33	chr6:29762010-29762060	U87	brain:	n/a
34	chr6:29762010-29762060	HCM	heart:	n/a
35	chr6:29762010-29762060	Hepatocyte	liver:	n/a
36	chr6:29762010-29762060	SAEC	small airway:	n/a
37	chr6:29762010-29762060	K562	blood:	n/a
38	chr6:29762010-29762060	MCF-7	breast:	n/a
39	chr6:29762010-29762060	NT2-D1	testis:	n/a
40	chr6:29762010-29762060	Hela-S3	cervix:	n/a
41	chr6:29762010-29762060	LNCaP	prostate:	n/a
42	chr6:29762010-29762060	HRPEpiC	eye:	n/a
43	chr6:29762010-29762060	IMR90	lung:	fetal
44	chr6:29762010-29762060	HRCEpiC	kidney:	n/a
45	chr6:29762010-29762060	HIPEpiC	eye:	n/a
46	chr6:29762010-29762060	HUVEC	blood vessel:	n/a
47	chr6:29762010-29762060	T-47D	breast:	n/a
48	chr6:29762010-29762060	HNPCEpiC	eye:	n/a
49	chr6:29762010-29762060	NHDF-neo	bronchial:	n/a
50	chr6:29762010-29762060	ProgFib	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29760873..29763751-chr6:29786445..29789008,2	MCF-7	breast:

No data

Variant related genes	Relation type
HCG4	CpG island

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12662918	0.96[ASN][1000 genomes]
rs3778614	0.96[ASN][1000 genomes]
rs3873238	0.89[ASN][1000 genomes]
rs3873243	0.81[ASN][1000 genomes]
rs4122198	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431305	0.87[ASN][1000 genomes]
rs9258293	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258295	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258302	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258303	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258436	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised 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	28 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv883537	chr6:29746023-29767611	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv883539	chr6:29748206-29780529	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29760400-29764400	Weak transcription	Hela-S3	cervix
2	chr6:29761000-29763000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:29761000-29765200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:29761200-29762200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:29761200-29763800	Weak transcription	HMEC	breast
6	chr6:29761200-29763800	Weak transcription	NHEK	skin
7	chr6:29761200-29764400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:29761400-29763800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:29761800-29766200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links