Variant report

Variant	rs200470
Chromosome Location	chr6:27762187-27762188
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27100250..27106326-chr6:27760451..27766140,11	K562	blood:
2	chr6:27484707..27486916-chr6:27761947..27763792,2	MCF-7	breast:
3	chr6:27100655..27103990-chr6:27762026..27765564,3	K562	blood:
4	chr6:27753667..27756583-chr6:27759368..27762944,3	MCF-7	breast:
5	chr6:27518478..27520972-chr6:27761797..27763366,2	K562	blood:
6	chr6:27113327..27117617-chr6:27761285..27764881,4	MCF-7	breast:
7	chr6:27759954..27762609-chr6:27862725..27865000,3	MCF-7	breast:
8	chr6:27199807..27202562-chr6:27760063..27762279,2	MCF-7	breast:
9	chr6:27112343..27120362-chr6:27757252..27765476,17	K562	blood:
10	chr6:27111619..27120059-chr6:27760198..27767915,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs187995	1.00[EUR][1000 genomes]
rs200472	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200947	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200955	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200959	1.00[EUR][1000 genomes]
rs200982	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200984	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201003	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201005	0.83[LWK][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56342784	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59716769	1.00[EUR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs200470	GSG1	trans	brain	seeQTL
rs200470	ASMT	trans	brain	seeQTL
rs200470	TTR	trans	brain	seeQTL
rs200470	PDE6H	trans	brain	seeQTL
rs200470	Hs.158943	cis	multi-tissue	Pritchard
rs200470	GUCA1C	trans	brain	seeQTL
rs200470	DEFB119	trans	brain	seeQTL
rs200470	DDC	trans	brain	seeQTL
rs200470	SH2D2A	trans	brain	seeQTL
rs200470	OTX2	trans	brain	seeQTL
rs200470	CRX	trans	brain	seeQTL
rs200470	SLC5A7	trans	brain	seeQTL
rs200470	LRTM1	trans	brain	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27760600-27763800	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:27760800-27764000	Weak transcription	Lung	lung
3	chr6:27761000-27763600	Enhancers	Fetal Intestine Small	intestine
4	chr6:27761200-27762200	Enhancers	GM12878-XiMat	blood
5	chr6:27761200-27763400	Weak transcription	HMEC	breast
6	chr6:27761200-27763600	Enhancers	Duodenum Mucosa	Duodenum
7	chr6:27761200-27763600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:27761200-27763800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:27761200-27763800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:27761200-27763800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:27761200-27763800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:27761200-27763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:27761200-27763800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:27761200-27764000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:27761200-27764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:27761200-27764000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:27761200-27764000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:27761200-27764000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:27761200-27764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:27761200-27764200	Enhancers	Fetal Intestine Large	intestine
21	chr6:27761200-27765000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:27761200-27768600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:27761400-27762200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr6:27761400-27763400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:27761400-27763400	Enhancers	K562	blood
26	chr6:27761400-27763800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:27761400-27763800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:27761400-27763800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:27761600-27762200	Enhancers	HepG2	liver
30	chr6:27761600-27762400	Enhancers	Hela-S3	cervix
31	chr6:27761600-27763400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:27761600-27763800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:27761600-27764000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:27761600-27768600	Weak transcription	NHEK	skin
35	chr6:27761800-27764200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:27762000-27763400	Weak transcription	Fetal Lung	lung
37	chr6:27762000-27764200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:27762000-27764200	Weak transcription	Brain Germinal Matrix	brain

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