Variant report

Variant	rs200955
Chromosome Location	chr6:27839312-27839313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:119)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:119 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27838549-27841707	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr6:27838747-27841649	PBDE	blood:	n/a	n/a
3	SIN3AK20	chr6:27838964-27840391	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr6:27839297-27840460	MCF10A-Er-Src	breast:	n/a	n/a
5	POU2F2	chr6:27839041-27839405	GM12891	blood:	n/a	n/a
6	MTA3	chr6:27838567-27841844	GM12878	blood:	n/a	n/a
7	TAF7	chr6:27839104-27840304	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:27838887-27840415	MCF-7	breast:	n/a	n/a
9	RELA	chr6:27838795-27841703	GM10847	blood:	n/a	n/a
10	NFIC	chr6:27839175-27841922	GM12878	blood:	n/a	n/a
11	ZBTB33	chr6:27839174-27840349	A549	lung:	n/a	n/a
12	TCF3	chr6:27839309-27840182	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:27839057-27839405	A549	lung:	n/a	n/a
14	RELA	chr6:27839203-27841750	GM18505	blood:	n/a	n/a
15	POLR2A	chr6:27839125-27840442	U87	brain:	n/a	n/a
16	POLR2A	chr6:27838660-27841777	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:27838603-27840485	MCF-7	breast:	n/a	n/a
18	POLR2A	chr6:27839242-27839338	A549	lung:	n/a	n/a
19	POLR2A	chr6:27838847-27841489	GM12892	blood:	n/a	n/a
20	POU2F2	chr6:27838996-27840341	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:27838878-27840417	MCF-7	breast:	n/a	n/a
22	POLR2A	chr6:27839119-27839365	A549	lung:	n/a	n/a
23	POLR2A	chr6:27839111-27840330	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:27838335-27841780	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr6:27839052-27841717	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr6:27838719-27841562	GM18951	blood:	n/a	n/a
27	POLR2A	chr6:27838702-27841553	GM19099	blood:	n/a	n/a
28	GATA1	chr6:27838875-27842026	PBDE	blood:	n/a	chr6:27839447-27839463 chr6:27839450-27839460 chr6:27839451-27839460 chr6:27839449-27839461
29	POLR2A	chr6:27838742-27841834	HUVEC	blood vessel:	n/a	n/a
30	ZNF143	chr6:27839206-27839395	H1-hESC	embryonic stem cell:	n/a	n/a
31	JUND	chr6:27839129-27840235	H1-hESC	embryonic stem cell:	n/a	chr6:27840171-27840180
32	MAX	chr6:27839301-27839589	H1-hESC	embryonic stem cell:	n/a	n/a
33	GATA3	chr6:27839097-27839780	A549	lung:	n/a	chr6:27839447-27839463 chr6:27839450-27839460 chr6:27839451-27839460 chr6:27839449-27839461
34	POLR2A	chr6:27838966-27840318	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:27838793-27841503	GM10847	blood:	n/a	n/a
36	TAF7	chr6:27838090-27841565	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr6:27838976-27840352	GM12892	blood:	n/a	n/a
38	CHD1	chr6:27838503-27841785	H1-hESC	embryonic stem cell:	n/a	n/a
39	PML	chr6:27839273-27840314	GM12878	blood:	n/a	n/a
40	NFIC	chr6:27839231-27841620	GM12878	blood:	n/a	n/a
41	BCLAF1	chr6:27839071-27841811	GM12878	blood:	n/a	chr6:27839452-27839459
42	SIN3AK20	chr6:27839152-27840369	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:27838984-27840265	GM12878	blood:	n/a	n/a
44	BCLAF1	chr6:27839173-27840326	GM12878	blood:	n/a	chr6:27839452-27839459
45	POLR2A	chr6:27838856-27841505	GM15510	blood:	n/a	n/a
46	POLR2A	chr6:27838729-27841503	GM18505	blood:	n/a	n/a
47	SP1	chr6:27839211-27839781	A549	lung:	n/a	n/a
48	POLR2A	chr6:27839100-27840332	GM12891	blood:	n/a	n/a
49	STAT5A	chr6:27839210-27840263	GM12878	blood:	n/a	n/a
50	CREB1	chr6:27838838-27840469	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26053886..26056754-chr6:27838528..27841562,3	MCF-7	breast:
2	chr6:27098237..27102845-chr6:27835694..27840254,5	MCF-7	breast:
3	chr1:149813872..149815940-chr6:27838697..27841107,2	MCF-7	breast:
4	chr6:26044692..26047309-chr6:27838299..27842021,15	MCF-7	breast:
5	chr17:57914621..57917067-chr6:27838760..27840646,2	MCF-7	breast:
6	chr6:27100852..27101558-chr6:27839278..27840055,2	NB4	blood:
7	chr6:26031607..26034880-chr6:27837430..27841431,3	K562	blood:
8	chr6:26044526..26047786-chr6:27838310..27841317,7	MCF-7	breast:
9	chr6:27838398..27840922-chr8:145149536..145152050,2	MCF-7	breast:
10	chr17:57922571..57924385-chr6:27837203..27839996,2	MCF-7	breast:
11	chr1:16839419..16842042-chr6:27838981..27840921,2	MCF-7	breast:
12	chr6:26268562..26271550-chr6:27838233..27840069,2	MCF-7	breast:
13	chr6:27837988..27840286-chr7:80547684..80550334,2	MCF-7	breast:
14	chr12:59313255..59314867-chr6:27838598..27840298,2	MCF-7	breast:
15	chr6:26025188..26029060-chr6:27836295..27841543,4	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H1B	TF binding region
ENSG00000075223	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000257443	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000139263	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000183558	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000179091	Chromatin interaction
ENSG00000187837	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs156741	1.00[TSI][hapmap]
rs156742	1.00[TSI][hapmap]
rs16867901	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16867911	1.00[TSI][hapmap]
rs169263	1.00[TSI][hapmap]
rs175597	0.96[MKK][hapmap];0.82[YRI][hapmap]
rs187995	1.00[EUR][1000 genomes]
rs200470	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200472	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200484	0.92[MKK][hapmap]
rs200487	1.00[ASW][hapmap];0.93[YRI][hapmap]
rs200501	0.92[MKK][hapmap]
rs200947	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200948	0.96[MKK][hapmap];0.88[YRI][hapmap]
rs200954	0.82[YRI][hapmap]
rs200959	0.84[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200965	0.88[YRI][hapmap]
rs200968	0.81[MKK][hapmap]
rs200970	1.00[TSI][hapmap]
rs200977	0.82[YRI][hapmap]
rs200982	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200984	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200989	0.96[MKK][hapmap];0.82[YRI][hapmap]
rs200995	0.81[MKK][hapmap]
rs201003	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201005	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2747054	0.92[MKK][hapmap]
rs276364	1.00[TSI][hapmap]
rs401763	0.84[MKK][hapmap]
rs56342784	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59716769	1.00[EUR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9295739	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs200955	PDE6H	trans	brain	seeQTL
rs200955	CRX	trans	brain	seeQTL
rs200955	TTR	trans	brain	seeQTL
rs200955	OTX2	trans	brain	seeQTL
rs200955	SLC5A7	trans	brain	seeQTL
rs200955	GSG1	trans	brain	seeQTL
rs200955	SH2D2A	trans	brain	seeQTL
rs200955	ASMT	trans	brain	seeQTL
rs200955	Hs.158943	cis	multi-tissue	Pritchard
rs200955	GUCA1C	trans	brain	seeQTL
rs200955	LRTM1	trans	brain	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27835400-27839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:27835400-27839600	Weak transcription	Colonic Mucosa	Colon
3	chr6:27835400-27839600	Weak transcription	Esophagus	oesophagus
4	chr6:27835400-27839600	Weak transcription	Pancreas	Pancrea
5	chr6:27835600-27839400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:27835600-27839400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:27835600-27839600	Weak transcription	Placenta	Placenta
8	chr6:27835600-27839600	Weak transcription	Right Ventricle	heart
9	chr6:27835600-27839600	Weak transcription	Spleen	Spleen
10	chr6:27835600-27839600	Weak transcription	HSMMtube	muscle
11	chr6:27835800-27839400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:27835800-27839400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:27835800-27839400	Weak transcription	Liver	Liver
14	chr6:27835800-27839400	Weak transcription	Fetal Heart	heart
15	chr6:27835800-27839400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:27835800-27839600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:27836000-27839400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:27836000-27839400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:27836000-27839400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:27836000-27839400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:27836000-27839400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:27836000-27839400	Weak transcription	A549	lung
23	chr6:27836000-27839400	Weak transcription	Osteobl	bone
24	chr6:27838200-27839400	Active TSS	Brain Germinal Matrix	brain
25	chr6:27838200-27839400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:27838200-27839800	Flanking Active TSS	Dnd41	blood
27	chr6:27838200-27839800	Enhancers	K562	blood
28	chr6:27838200-27842000	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr6:27838400-27839400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:27838400-27839600	Weak transcription	Lung	lung
31	chr6:27838600-27839400	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:27838600-27842400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr6:27838800-27839400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:27838800-27839400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:27838800-27839400	Enhancers	Primary B cells from cord blood	blood
36	chr6:27838800-27839400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr6:27838800-27840800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:27838800-27841000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:27838800-27841400	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:27838800-27842400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:27839000-27839400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:27839000-27839400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:27839000-27839400	Enhancers	Primary B cells from peripheral blood	blood
44	chr6:27839000-27839400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr6:27839000-27839400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:27839000-27839400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:27839000-27839400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:27839000-27839400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr6:27839000-27839400	Enhancers	GM12878-XiMat	blood
50	chr6:27839000-27839600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links