Variant report

Variant	rs9468805
Chromosome Location	chr6:30643709-30643710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30642917-30644147	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:30643576-30644234	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:30643602-30644084	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:30643542-30644123	K562	blood:	n/a	n/a
5	PML	chr6:30643626-30644313	K562	blood:	n/a	n/a
6	POLR2A	chr6:30643532-30644606	K562	blood:	n/a	n/a
7	POLR2A	chr6:30643573-30644447	GM12891	blood:	n/a	n/a
8	BCLAF1	chr6:30643517-30643964	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:30642654-30644088	U87	brain:	n/a	n/a
10	POLR2A	chr6:30643546-30643995	GM12891	blood:	n/a	n/a
11	MTA3	chr6:30643461-30644136	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:30643446-30644161	HUVEC	blood vessel:	n/a	n/a
13	PML	chr6:30643447-30644199	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:30643481-30644007	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr6:30643236-30644104	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr6:30643681-30643939	ProgFib	skin:	n/a	n/a
17	POLR2A	chr6:30643367-30645364	PFSK-1	brain:	n/a	n/a
18	NFATC1	chr6:30643502-30643819	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:30643612-30644122	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:30643567-30643887	U87	brain:	n/a	n/a
21	POLR2A	chr6:30642648-30644094	U87	brain:	n/a	n/a
22	POLR2A	chr6:30643671-30643725	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr6:30643440-30645279	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:30643589-30644122	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:30643530-30644106	GM12892	blood:	n/a	n/a
26	POLR2A	chr6:30643515-30644080	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr6:30643620-30644176	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:30643425-30644035	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr6:30643455-30644135	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30643140..30646430-chr6:30646778..30649546,3	MCF-7	breast:
2	chr6:30642982..30645092-chr6:30648552..30650727,2	MCF-7	breast:
3	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
4	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
5	chr6:30639491..30642399-chr6:30642819..30647161,4	MCF-7	breast:
6	chr6:30642470..30648471-chr6:30697241..30700740,8	MCF-7	breast:
7	chr6:30581230..30587315-chr6:30638443..30644329,12	MCF-7	breast:
8	chr6:30577127..30589352-chr6:30620628..30648657,88	K562	blood:
9	chr6:30582956..30585804-chr6:30643199..30647453,3	MCF-7	breast:

No data

Variant related genes	Relation type
DHX16	TF binding region
ENSG00000204569	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000196230	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1079687	0.94[ASN][1000 genomes]
rs1109146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16897781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16897791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075015	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239886	0.88[ASN][1000 genomes]
rs2269702	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284172	0.82[EUR][1000 genomes]
rs2285321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394392	0.94[ASN][1000 genomes]
rs25497	0.82[EUR][1000 genomes]
rs28986465	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3094090	0.86[ASN][1000 genomes]
rs3132595	0.94[ASN][1000 genomes]
rs3132608	0.94[ASN][1000 genomes]
rs55810373	0.82[EUR][1000 genomes]
rs59378621	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61486053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61733213	0.88[AFR][1000 genomes]
rs6900113	0.83[AFR][1000 genomes]
rs6924270	0.88[ASN][1000 genomes]
rs6929626	0.88[ASN][1000 genomes]
rs6929698	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6931293	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6937357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762626	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7773711	0.89[AFR][1000 genomes]
rs9295901	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295905	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295908	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295909	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461623	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461624	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461625	0.82[EUR][1000 genomes]
rs9468803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468807	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9468811	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468812	0.88[AFR][1000 genomes]
rs9468813	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468814	0.88[ASN][1000 genomes]
rs9468816	0.82[EUR][1000 genomes]
rs9468817	0.82[EUR][1000 genomes]
rs9500863	0.82[EUR][1000 genomes]
rs9500866	0.82[EUR][1000 genomes]
rs9500867	0.82[EUR][1000 genomes]
rs9501027	0.82[EUR][1000 genomes]
rs9501338	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9501481	0.88[ASN][1000 genomes]
rs9501482	0.88[ASN][1000 genomes]
rs9501483	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9501484	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
6	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv823472	chr6:30638581-30644218	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30640800-30643800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:30640800-30643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:30640800-30643800	Weak transcription	Lung	lung
4	chr6:30640800-30643800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:30640800-30643800	Weak transcription	Small Intestine	intestine
6	chr6:30640800-30643800	Weak transcription	Spleen	Spleen
7	chr6:30640800-30643800	Weak transcription	NHDF-Ad	bronchial
8	chr6:30640800-30644000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:30640800-30644000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:30640800-30644000	Weak transcription	Esophagus	oesophagus
11	chr6:30640800-30644000	Weak transcription	Pancreas	Pancrea
12	chr6:30640800-30644400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:30640800-30644400	Weak transcription	Aorta	Aorta
14	chr6:30640800-30644400	Weak transcription	Gastric	stomach
15	chr6:30640800-30647000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:30640800-30649600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:30641000-30643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:30641000-30643800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:30641000-30643800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:30641000-30643800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:30641000-30643800	Weak transcription	Placenta	Placenta
22	chr6:30641000-30643800	Weak transcription	Left Ventricle	heart
23	chr6:30641000-30643800	Weak transcription	Ovary	ovary
24	chr6:30641000-30643800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:30641000-30644000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:30641000-30644000	Weak transcription	Colonic Mucosa	Colon
27	chr6:30641000-30644000	Weak transcription	Right Ventricle	heart
28	chr6:30641000-30644200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:30641000-30644400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:30641000-30644400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:30641000-30644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:30641000-30647000	Weak transcription	Stomach Mucosa	stomach
33	chr6:30641000-30647600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:30641000-30650000	Weak transcription	Psoas Muscle	Psoas
35	chr6:30641200-30643800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:30641200-30643800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:30641200-30643800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:30641200-30643800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:30641200-30643800	Weak transcription	Primary T cells from cord blood	blood
40	chr6:30641200-30643800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:30641200-30643800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:30641200-30643800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:30641200-30643800	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:30641200-30643800	Weak transcription	Fetal Intestine Large	intestine
45	chr6:30641200-30643800	Weak transcription	Fetal Intestine Small	intestine
46	chr6:30641200-30643800	Weak transcription	Fetal Lung	lung
47	chr6:30641200-30643800	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:30641200-30643800	Weak transcription	Fetal Stomach	stomach
49	chr6:30641200-30643800	Weak transcription	GM12878-XiMat	blood
50	chr6:30641200-30643800	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links