Variant report

Variant	rs9295898
Chromosome Location	chr6:30449046-30449047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30449040-30449190	HA-sp	spinal cord:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
2	CTCF	chr6:30448940-30449090	GM12871	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
3	CTCF	chr6:30448980-30449130	HBMEC	blood vessel:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
4	CTCF	chr6:30449000-30449150	HRE	kidney:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
5	CTCF	chr6:30448960-30449110	HPAF	blood vessel:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
6	CTCF	chr6:30449020-30449170	WERI-Rb-1	eye:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
7	CTCF	chr6:30449040-30449190	HFF-Myc	foreskin:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
8	CTCF	chr6:30448993-30449158	GM12891	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
9	CTCF	chr6:30448960-30449110	AG09319	gingival:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
10	CTCF	chr6:30449025-30449123	GM19239	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
11	CTCF	chr6:30448984-30449199	K562	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
12	CTCF	chr6:30449000-30449150	HUVEC	blood vessel:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
13	CTCF	chr6:30448938-30449281	K562	blood:	n/a	chr6:30449066-30449082 chr6:30449226-30449235 chr6:30449067-30449080
14	CTCF	chr6:30448960-30449110	GM06990	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
15	CTCF	chr6:30448980-30449130	GM12866	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
16	CTCF	chr6:30449040-30449190	HRPEpiC	eye:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
17	CTCF	chr6:30448980-30449130	AG04449	skin:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
18	CTCF	chr6:30449021-30449150	GM19240	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
19	CTCF	chr6:30448729-30450259	SK-N-SH	brain:	n/a	chr6:30449066-30449082 chr6:30449226-30449235 chr6:30449067-30449080 chr6:30449344-30449352
20	CTCF	chr6:30449040-30449190	GM12869	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
21	CTCF	chr6:30449028-30449108	Fibrobl	skin:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
22	CTCF	chr6:30448939-30449190	K562	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
23	CTCF	chr6:30448940-30449090	K562	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
24	CTCF	chr6:30449000-30449141	GM19238	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
25	CTCF	chr6:30449030-30449155	Spleen_OC	spleen:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
26	CTCF	chr6:30448900-30449050	GM12872	blood:	n/a	n/a
27	CTCF	chr6:30449020-30449170	RPTEC	kidney:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
28	CTCF	chr6:30448960-30449110	HCM	heart:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
29	CTCF	chr6:30449000-30449150	GM12868	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
30	CTCF	chr6:30449020-30449170	GM12865	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
31	CTCF	chr6:30449000-30449150	WERI-Rb-1	eye:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
32	CTCF	chr6:30449036-30449105	K562	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
33	CTCF	chr6:30448900-30449050	GM06990	blood:	n/a	n/a
34	CTCF	chr6:30448979-30449180	SK-N-SH_RA	brain:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
35	CTCF	chr6:30449040-30449190	K562	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
36	CTCF	chr6:30449000-30449150	GM12874	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
37	RAD21	chr6:30448910-30449156	HepG2	liver:	n/a	n/a
38	CTCF	chr6:30449012-30449129	GM12892	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
39	RAD21	chr6:30449018-30449139	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr6:30448942-30449194	HepG2	liver:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
41	CTCF	chr6:30449020-30449170	HCPEpiC	choroid plexus:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
42	CTCF	chr6:30448968-30449203	H1-hESC	embryonic stem cell:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
43	CTCF	chr6:30448980-30449130	AG04450	lung:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
44	CTCF	chr6:30448920-30449070	HFF	foreskin:	n/a	n/a
45	CTCF	chr6:30448980-30449130	HMEC	breast:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
46	CTCF	chr6:30448980-30449130	GM12867	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
47	CTCF	chr6:30449000-30449150	Caco-2	colon:	n/a	chr6:30449066-30449082 chr6:30449067-30449080
48	CTCF	chr6:30449045-30449160	GM12878	blood:	n/a	chr6:30449066-30449082 chr6:30449067-30449080

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30449009-30449059	U87	brain:	n/a
2	chr6:30449009-30449059	H1-hESC	embryonic stem cell:	embryo
3	chr6:30449009-30449059	SK-N-MC	brain:	n/a
4	chr6:30449009-30449059	AG09309	skin:	n/a
5	chr6:30449009-30449059	SKMC	muscle:	n/a
6	chr6:30449009-30449059	HPAEpiC	pulmonary alveolar:	n/a
7	chr6:30449009-30449059	BJ	skin:	n/a
8	chr6:30449009-30449059	HCF	heart:	n/a
9	chr6:30449009-30449059	HUVEC	blood vessel:	n/a
10	chr6:30449009-30449059	AG04449	skin:	fetal
11	chr6:30449009-30449059	ovcar-3	ovarian:	n/a
12	chr6:30449009-30449059	BE2_C	brain:	n/a
13	chr6:30449009-30449059	ECC-1	luminal epithelium:	n/a
14	chr6:30449009-30449059	HRE	kidney:	n/a
15	chr6:30449009-30449059	RPTEC	kidney:	n/a
16	chr6:30449009-30449059	HepG2	liver:	n/a
17	chr6:30449009-30449059	NB4	blood:	n/a
18	chr6:30449009-30449059	Caco-2	colon:	n/a
19	chr6:30449009-30449059	MCF-7	breast:	n/a
20	chr6:30449009-30449059	GM12878	blood:	n/a
21	chr6:30449009-30449059	NHBE	bronchial:	n/a
22	chr6:30449009-30449059	HIPEpiC	eye:	n/a
23	chr6:30449009-30449059	Hepatocyte	liver:	n/a
24	chr6:30449009-30449059	HL-60	blood:	n/a
25	chr6:30449009-30449059	SK-N-SH	brain:	n/a
26	chr6:30449009-30449059	HNPCEpiC	eye:	n/a
27	chr6:30449009-30449059	GM19239	blood:	n/a
28	chr6:30449009-30449059	HCPEpiC	choroid plexus:	n/a
29	chr6:30449009-30449059	HEK293	kidney:	embryo
30	chr6:30449009-30449059	NT2-D1	testis:	n/a
31	chr6:30449009-30449059	GM12891	blood:	n/a
32	chr6:30449009-30449059	HMEC	breast:	n/a
33	chr6:30449009-30449059	GM12892	blood:	n/a
34	chr6:30449009-30449059	NH-A	brain:	n/a
35	chr6:30449009-30449059	AG09319	gingival:	n/a
36	chr6:30449009-30449059	T-47D	breast:	n/a
37	chr6:30449009-30449059	HRPEpiC	eye:	n/a
38	chr6:30449009-30449059	AG04450	lung:	fetal
39	chr6:30449009-30449059	CMK	blood:	n/a
40	chr6:30449009-30449059	SK-N-SH_RA	brain:	n/a
41	chr6:30449009-30449059	A549	lung:	n/a
42	chr6:30449009-30449059	AoSMC	blood vessel:	n/a
43	chr6:30449009-30449059	Hela-S3	cervix:	n/a
44	chr6:30449009-30449059	NHDF-neo	bronchial:	n/a
45	chr6:30449009-30449059	IMR90	lung:	fetal
46	chr6:30449009-30449059	MCF10A-Er-Src	breast:	n/a
47	chr6:30449009-30449059	SAEC	small airway:	n/a
48	chr6:30449009-30449059	LNCaP	prostate:	n/a
49	chr6:30449009-30449059	PrEC	prostate:	n/a
50	chr6:30449009-30449059	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30447797..30449612-chr6:30512660..30515323,2	MCF-7	breast:
2	chr6:30448465..30450230-chr6:30522710..30525074,2	K562	blood:
3	chr6:30447631..30450065-chr6:30691817..30695001,3	K562	blood:
4	chr6:30422351..30425241-chr6:30448232..30450888,2	MCF-7	breast:
5	chr6:30446384..30451689-chr6:30578094..30585004,12	MCF-7	breast:
6	chr6:30447476..30449412-chr6:30509865..30511998,2	K562	blood:
7	chr6:30448715..30451618-chr6:30508372..30511107,3	MCF-7	breast:
8	chr6:30448170..30453321-chr6:30582822..30586539,6	K562	blood:
9	chr6:30447949..30451648-chr6:30569801..30572499,4	MCF-7	breast:

Variant related genes	Relation type
RANP1	TF binding region
RANP1	CpG island
ENSG00000204590	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2021719	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2021720	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2105960	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2524192	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711220	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6921669	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7747873	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7761083	0.84[AFR][1000 genomes]
rs7761210	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7764934	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7775268	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295899	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380180	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv884069	chr6:30430875-30451474	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv884070	chr6:30430875-30472772	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
7	nsv884075	chr6:30434566-30449046	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv884076	chr6:30434566-30483919	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9295898	GRM4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30447800-30450200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:30448000-30449800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
3	chr6:30448000-30450000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
4	chr6:30448000-30450200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:30448000-30450200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr6:30448000-30450200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:30448200-30449200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr6:30448200-30449200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:30448200-30449200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr6:30448200-30449200	Flanking Bivalent TSS/Enh	NHEK	skin
11	chr6:30448200-30449600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
12	chr6:30448200-30450000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:30448200-30450000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
14	chr6:30448200-30450000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
15	chr6:30448200-30450000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
16	chr6:30448200-30450000	Bivalent Enhancer	Fetal Thymus	thymus
17	chr6:30448200-30450000	Bivalent Enhancer	GM12878-XiMat	blood
18	chr6:30448200-30450200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:30448200-30450400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr6:30448400-30449600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:30448400-30449800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr6:30448400-30449800	Bivalent Enhancer	HUVEC	blood vessel
23	chr6:30448400-30450000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:30448400-30450000	Bivalent Enhancer	Primary B cells from cord blood	blood
25	chr6:30448400-30450000	Enhancers	Spleen	Spleen
26	chr6:30448400-30450000	Bivalent Enhancer	HMEC	breast
27	chr6:30448400-30450400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr6:30448600-30449400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:30448600-30449600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:30448600-30449600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:30448600-30449800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:30448600-30450000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
33	chr6:30448800-30449200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr6:30448800-30449200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:30448800-30449200	Bivalent Enhancer	Liver	Liver
36	chr6:30448800-30449400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:30448800-30449400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:30448800-30449600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:30448800-30449600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:30448800-30449800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
41	chr6:30448800-30450000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:30448800-30450000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr6:30448800-30450000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:30448800-30450200	Bivalent Enhancer	Fetal Stomach	stomach
45	chr6:30449000-30449200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:30449000-30449200	Bivalent Enhancer	Primary T cells from cord blood	blood
47	chr6:30449000-30449200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr6:30449000-30449200	Flanking Bivalent TSS/Enh	A549	lung
49	chr6:30449000-30449400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:30449000-30449400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin

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