Variant report

Variant	rs1233664
Chromosome Location	chr6:28185726-28185727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28184931..28189194-chr6:28190077..28194573,12	MCF-7	breast:
2	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
3	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
4	chr6:28108272..28111912-chr6:28184259..28187979,3	MCF-7	breast:
5	chr6:28185564..28187470-chr6:28218621..28220714,2	MCF-7	breast:
6	chr6:27805809..27807448-chr6:28184413..28187037,2	MCF-7	breast:
7	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
8	chr6:27774472..27777190-chr6:28183511..28185747,2	K562	blood:
9	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
10	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
11	chr6:28104139..28106070-chr6:28185714..28187223,2	MCF-7	breast:
12	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
13	chr6:28184805..28186411-chr6:28255755..28258597,2	K562	blood:
14	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
15	chr6:28184440..28186086-chr6:28227732..28230449,2	K562	blood:
16	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
17	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233822	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10484404	0.90[CEU][hapmap]
rs1062169	0.94[GIH][hapmap];0.83[TSI][hapmap]
rs1150697	0.81[CEU][hapmap]
rs1150698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs1150714	0.80[CEU][hapmap]
rs11752073	0.90[CEU][hapmap]
rs11758148	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1233665	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474589	0.80[CEU][hapmap]
rs16893817	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16893937	0.80[CEU][hapmap]
rs16901846	0.80[CEU][hapmap]
rs1736890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736894	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778469	0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778477	0.94[GIH][hapmap]
rs1890809	0.90[CEU][hapmap]
rs2232422	0.80[CEU][hapmap]
rs2281043	0.80[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs2622315	0.90[CEU][hapmap]
rs3800325	0.80[CEU][hapmap]
rs6456811	0.80[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs6917759	0.90[CEU][hapmap]
rs6923170	0.80[CEU][hapmap]
rs6929559	0.90[CEU][hapmap]
rs73740584	0.96[EUR][1000 genomes]
rs73740587	0.90[EUR][1000 genomes]
rs7744788	0.80[CEU][hapmap]
rs7769054	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs993619	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][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	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv527115	chr6:28185726-28186554	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1233664	PARD6B	trans	cerebellum	SCAN
rs1233664	ZNF323	cis	parietal	SCAN
rs1233664	ZNF192P1	cis	Adipose Subcutaneous	GTEx
rs1233664	ZSCAN23	cis	parietal	SCAN
rs1233664	ZNF165	cis	parietal	SCAN
rs1233664	HIST1H4C	cis	parietal	SCAN
rs1233664	AL022393.7	cis	Thyroid	GTEx
rs1233664	HFE	cis	cerebellum	SCAN
rs1233664	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28180800-28186400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28181400-28186000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:28181400-28186000	Weak transcription	HSMM	muscle
4	chr6:28182800-28186000	Enhancers	Placenta	Placenta
5	chr6:28183600-28186000	Weak transcription	HMEC	breast
6	chr6:28183600-28186200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:28183800-28185800	Enhancers	HepG2	liver
8	chr6:28184000-28185800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28184000-28186000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:28184000-28186000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:28184200-28185800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:28184600-28186000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr6:28184600-28186600	Enhancers	Spleen	Spleen
14	chr6:28184800-28185800	Enhancers	Right Ventricle	heart
15	chr6:28184800-28186000	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr6:28184800-28186200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:28184800-28186400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr6:28185000-28186000	Weak transcription	Gastric	stomach
19	chr6:28185000-28186000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:28185200-28185800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr6:28185200-28186000	Enhancers	Fetal Heart	heart
22	chr6:28185200-28186000	Weak transcription	Right Atrium	heart
23	chr6:28185200-28186400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr6:28185400-28185800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:28185400-28185800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:28185400-28186000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:28185400-28186000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr6:28185400-28186000	Enhancers	Left Ventricle	heart
29	chr6:28185400-28186200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:28185400-28186200	Flanking Active TSS	K562	blood
31	chr6:28185400-28186400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:28185400-28186400	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr6:28185600-28185800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr6:28185600-28185800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28185600-28185800	Enhancers	Esophagus	oesophagus
36	chr6:28185600-28186000	Enhancers	GM12878-XiMat	blood
37	chr6:28185600-28186200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:28185600-28186400	Flanking Active TSS	Hela-S3	cervix
39	chr6:28185600-28186600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:28185600-28187000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr6:28185600-28187400	Active TSS	Stomach Smooth Muscle	stomach

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