Variant report

Variant	rs10888428
Chromosome Location	chr1:151679900-151679901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151678147-151680594	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:151679642-151680959	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151582188..151584894-chr1:151679011..151681614,2	MCF-7	breast:
2	chr1:151677367..151680039-chr1:151802606..151805197,3	MCF-7	breast:
3	chr1:151678494..151680189-chr1:151689404..151690946,2	K562	blood:
4	chr1:151677595..151679984-chr1:151683063..151685340,3	K562	blood:

Variant related genes	Relation type
ENSG00000240510	TF binding region
RIIAD1	TF binding region
ENSG00000143376	Chromatin interaction
ENSG00000143365	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1048694	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204866	0.83[EUR][1000 genomes]
rs11586679	0.81[EUR][1000 genomes]
rs1196352	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1196357	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs1196459	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1196464	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196465	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1201651	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1211981	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1308137	0.88[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1308139	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1308143	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1308145	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1308146	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1308147	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1308148	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1308152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1308158	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1717128	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17641780	0.84[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1781434	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1891589	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2460996	0.86[EUR][1000 genomes]
rs2489892	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2495392	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2495393	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2495394	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3204344	0.88[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3790512	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684548	0.85[EUR][1000 genomes]
rs6685067	0.88[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6687866	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6702842	0.87[CEU][hapmap];0.91[TSI][hapmap]
rs7534887	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10888428	LYSMD1	cis	parietal	SCAN
rs10888428	PLEKHO1	cis	cerebellum	SCAN
rs10888428	LINGO4	cis	cerebellum	SCAN
rs10888428	TDRKH	cis	cerebellum	SCAN
rs10888428	TDRKH	cis	parietal	SCAN
rs10888428	LCE1C	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151663200-151683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:151666000-151685400	Weak transcription	A549	lung
3	chr1:151667000-151687400	Weak transcription	K562	blood
4	chr1:151667800-151686000	Weak transcription	HMEC	breast
5	chr1:151669600-151681200	Strong transcription	Fetal Brain Female	brain
6	chr1:151670000-151689800	Weak transcription	Pancreas	Pancrea
7	chr1:151671400-151682600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:151672200-151680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:151672400-151684800	Weak transcription	Small Intestine	intestine
10	chr1:151673800-151680400	Strong transcription	Fetal Intestine Large	intestine
11	chr1:151673800-151682400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:151673800-151685200	Weak transcription	Fetal Kidney	kidney
13	chr1:151674000-151682400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:151674000-151685400	Weak transcription	Gastric	stomach
15	chr1:151674200-151683200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:151674200-151683200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:151674200-151687400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:151674600-151681800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:151674600-151682400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:151674600-151682600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:151674600-151683200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:151674600-151683200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:151674600-151685200	Weak transcription	Fetal Lung	lung
24	chr1:151674600-151686000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:151674800-151681800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:151674800-151686200	Weak transcription	Esophagus	oesophagus
27	chr1:151675400-151681400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:151675800-151681000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:151676200-151682400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:151676600-151680000	Weak transcription	Spleen	Spleen
31	chr1:151677000-151681800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:151678000-151682000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:151678200-151680400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:151678400-151680200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:151679000-151682000	Weak transcription	Brain Anterior Caudate	brain
36	chr1:151679200-151680200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr1:151679200-151682200	Strong transcription	Brain Germinal Matrix	brain
38	chr1:151679200-151684600	Weak transcription	Colonic Mucosa	Colon
39	chr1:151679400-151681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:151679400-151684400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:151679600-151680000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:151679600-151680600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:151679600-151680800	Weak transcription	Fetal Brain Male	brain
44	chr1:151679600-151681800	Strong transcription	Fetal Intestine Small	intestine
45	chr1:151679600-151684000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:151679600-151684800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:151679800-151680000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:151679800-151680000	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links