Variant report

Variant	rs200480
Chromosome Location	chr6:27773664-27773665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
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	TCF7L2	chr6:27773658-27774008	HepG2	liver:	n/a	n/a
2	NFE2	chr6:27773654-27773764	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:27773034-27773817	GM12878	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26203418..26208290-chr6:27773529..27778557,7	MCF-7	breast:
2	chr6:27356362..27358956-chr6:27773296..27775539,3	K562	blood:
3	chr2:242640497..242642008-chr6:27772593..27775464,2	MCF-7	breast:
4	chr6:27112242..27117659-chr6:27770082..27780470,17	MCF-7	breast:
5	chr6:27093369..27111594-chr6:27770152..27782376,64	K562	blood:
6	chr6:27638059..27640499-chr6:27771985..27774359,2	MCF-7	breast:
7	chr6:26282374..26290542-chr6:27772727..27779446,9	MCF-7	breast:
8	chr6:26216556..26218628-chr6:27772763..27774352,2	K562	blood:
9	chr6:26501647..26503357-chr6:27772900..27774524,2	K562	blood:
10	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
11	chr6:27128242..27130382-chr6:27772213..27774581,2	K562	blood:
12	chr4:74123460..74124971-chr6:27773658..27776230,2	MCF-7	breast:
13	chr6:26270357..26275628-chr6:27773210..27778290,5	MCF-7	breast:
14	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
15	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
16	chr6:26216294..26218815-chr6:27772946..27775743,3	MCF-7	breast:
17	chr6:27112544..27118917-chr6:27770503..27773854,7	K562	blood:
18	chr6:27513787..27515297-chr6:27772602..27774614,2	K562	blood:
19	chr6:26197916..26207803-chr6:27772547..27779655,13	K562	blood:

No data

Variant related genes	Relation type
HIST1H2AI	TF binding region
HIST1H4PS1	TF binding region
HIST1H3H	TF binding region
ENSG00000168274	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000250220	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000168395	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000168242	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000132466	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs200997	0.86[EUR][1000 genomes]
rs2056924	0.81[JPT][hapmap]
rs276362	0.91[CHB][hapmap]
rs4713120	0.93[ASW][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs57252182	0.80[ASN][1000 genomes]
rs6921256	0.81[JPT][hapmap]
rs9295747	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9348772	0.81[JPT][hapmap]
rs9380007	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs9393830	0.83[JPT][hapmap]
rs9393831	0.81[JPT][hapmap]
rs9468209	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs200480	ZNF323	cis	parietal	SCAN
rs200480	ZKSCAN3	cis	parietal	SCAN
rs200480	ZSCAN23	cis	Muscle Skeletal	GTEx
rs200480	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200480	HIST1H3I	cis	cerebellum	SCAN
rs200480	ZSCAN16	cis	parietal	SCAN
rs200480	ZNF323	cis	cerebellum	SCAN
rs200480	ZNF323	cis	brain	seeQTL
rs200480	ZSCAN23	cis	cerebellum	SCAN
rs200480	BTN3A3	cis	cerebellum	SCAN
rs200480	AL022393.7	cis	Muscle Skeletal	GTEx
rs200480	ZSCAN23	cis	lymphoblastoid	seeQTL
rs200480	ZNF323	cis	Frontal Cortex	GTEx
rs200480	ZNF204P	cis	parietal	SCAN
rs200480	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200480	ZNF192	cis	cerebellum	SCAN
rs200480	NKAPL	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27764400-27774200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:27769200-27774400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:27769200-27774400	Weak transcription	NHEK	skin
4	chr6:27769600-27774400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:27771800-27774400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:27772600-27773800	Flanking Active TSS	K562	blood
7	chr6:27773000-27774000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:27773400-27774200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:27773400-27775200	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:27773600-27774000	Enhancers	A549	lung
11	chr6:27773600-27774400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:27773600-27774400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links