Variant report

Variant	rs868868
Chromosome Location	chr1:151762108-151762109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:151762087-151764336	IMR90	lung:	n/a	n/a
2	MAX	chr1:151762096-151764240	MCF-7	breast:	n/a	chr1:151763829-151763839
3	RFX5	chr1:151760827-151765002	SK-N-SH	brain:	n/a	chr1:151761465-151761474
4	MXI1	chr1:151761776-151764760	SK-N-SH	brain:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151735509..151737891-chr1:151761737..151764631,3	K562	blood:
2	chr1:151760700..151764856-chr1:151797170..151799946,4	MCF-7	breast:
3	chr1:151736194..151739106-chr1:151761711..151764631,3	K562	blood:
4	chr1:151762059..151766604-chr1:151800169..151809078,15	MCF-7	breast:
5	chr1:151371873..151373520-chr1:151760428..151762155,2	K562	blood:
6	chr1:151042193..151044467-chr1:151761804..151763901,2	MCF-7	breast:
7	chr1:151761172..151762786-chr1:151788164..151789988,2	MCF-7	breast:
8	chr1:151733895..151739384-chr1:151759968..151766425,14	MCF-7	breast:
9	chr1:151739515..151742335-chr1:151761325..151763693,2	MCF-7	breast:
10	chr1:151583249..151586152-chr1:151761338..151763937,3	K562	blood:
11	chr1:151734278..151737585-chr1:151760529..151764689,8	MCF-7	breast:
12	chr1:151759662..151762835-chr1:151769243..151771568,4	K562	blood:
13	chr1:151760926..151765128-chr1:151802888..151806720,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203288	TF binding region
ENSG00000232937	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000249602	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000269489	Chromatin interaction
ENSG00000143450	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888435	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204885	0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11204887	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204888	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12066445	0.81[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12073999	0.91[EUR][1000 genomes]
rs12409493	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12567867	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1781419	0.88[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293088	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs33911740	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3748612	0.82[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923394	0.84[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4845572	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667279	0.93[EUR][1000 genomes]
rs6679233	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs7534811	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9017	0.96[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs9826	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs868868	TDRKH	cis	cerebellum	SCAN
rs868868	TDRKH	trans	multi-tissue	Pritchard
rs868868	BCL9	cis	cerebellum	SCAN
rs868868	TDRKH	cis	multi-tissue	Pritchard
rs868868	S100A13	cis	cerebellum	SCAN
rs868868	LINGO4	cis	cerebellum	SCAN
rs868868	TDRKH	cis	Liver	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736800-151762600	Weak transcription	Gastric	stomach
2	chr1:151737000-151762400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:151737000-151762400	Weak transcription	HSMMtube	muscle
4	chr1:151737000-151762600	Weak transcription	Small Intestine	intestine
5	chr1:151741000-151762600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:151742800-151762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:151744000-151762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:151744600-151762200	Weak transcription	Primary B cells from cord blood	blood
9	chr1:151746000-151762400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:151747000-151762400	Weak transcription	Psoas Muscle	Psoas
11	chr1:151747000-151762400	Weak transcription	Right Ventricle	heart
12	chr1:151747200-151762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:151747600-151762400	Weak transcription	Pancreas	Pancrea
14	chr1:151748400-151762200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:151748600-151762400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:151748800-151762400	Weak transcription	Colonic Mucosa	Colon
17	chr1:151749200-151762600	Weak transcription	Spleen	Spleen
18	chr1:151749400-151762400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:151749600-151762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:151749600-151762600	Weak transcription	Lung	lung
21	chr1:151751200-151762400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:151751400-151762200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:151751400-151762400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:151751600-151762200	Weak transcription	Brain Angular Gyrus	brain
25	chr1:151751600-151762400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:151752400-151762400	Weak transcription	Ovary	ovary
27	chr1:151752600-151762200	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:151752600-151762200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:151754200-151762200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:151754400-151762200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:151754400-151762400	Weak transcription	Placenta	Placenta
32	chr1:151754600-151762200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:151754600-151762400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:151755000-151762400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:151755400-151762200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:151755400-151762400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:151755400-151762600	Weak transcription	Aorta	Aorta
38	chr1:151755600-151762200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:151756200-151762400	Weak transcription	Left Ventricle	heart
40	chr1:151756400-151762200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:151757000-151762400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:151759200-151762200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:151759400-151762400	Weak transcription	Hela-S3	cervix
44	chr1:151761200-151762200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:151761200-151762200	Weak transcription	HMEC	breast
46	chr1:151761400-151762200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:151761600-151762400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr1:151761600-151763000	Flanking Active TSS	Dnd41	blood
49	chr1:151761800-151762200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr1:151761800-151762200	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links