Variant report

Variant	rs1211981
Chromosome Location	chr1:151632646-151632647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	1:151402394-151411623..1:151618750-151636526	GM12878	blood:
2	1:151171193-151178589..1:151618750-151636526	Hela-S3	cervix:
3	1:151592347-151603110..1:151618750-151636526	Hela-S3	cervix:
4	chr1:151630604..151632996-chr1:151635401..151638302,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206635	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1048694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888428	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]
rs11204866	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11586679	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196350	0.80[MEX][hapmap];0.89[MKK][hapmap]
rs1196352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1196357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1196459	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196464	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196465	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1201651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122920	0.84[MEX][hapmap]
rs1308137	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1308139	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1308143	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1308145	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1308146	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1308147	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1308148	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1308152	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1308158	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1717128	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17641780	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1781434	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1891589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1891591	0.82[ASN][1000 genomes]
rs2460996	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2489892	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2495392	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2495393	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495394	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3204344	0.96[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs34718348	0.82[EUR][1000 genomes]
rs35981950	0.84[EUR][1000 genomes]
rs3790512	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6684548	0.98[EUR][1000 genomes]
rs6685067	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6687866	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs6702842	0.95[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7534887	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv2843	chr1:151600069-151644709	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1211981	S100A4	cis	cerebellum	SCAN
rs1211981	LINGO4	cis	cerebellum	SCAN
rs1211981	LCE1C	cis	parietal	SCAN
rs1211981	TDRKH	cis	parietal	SCAN
rs1211981	PLEKHO1	cis	cerebellum	SCAN
rs1211981	TDRKH	cis	cerebellum	SCAN
rs1211981	BCL9	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151587600-151640600	Weak transcription	Fetal Brain Male	brain
2	chr1:151588200-151665200	Weak transcription	Aorta	Aorta
3	chr1:151591200-151675400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:151592600-151633800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:151594000-151652800	Weak transcription	Right Ventricle	heart
6	chr1:151603000-151663200	Weak transcription	Colonic Mucosa	Colon
7	chr1:151610200-151633800	Weak transcription	HUVEC	blood vessel
8	chr1:151610600-151652200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:151610600-151665000	Weak transcription	Lung	lung
10	chr1:151611600-151633000	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:151611600-151634200	Weak transcription	Psoas Muscle	Psoas
12	chr1:151611600-151637600	Weak transcription	Fetal Heart	heart
13	chr1:151611600-151639800	Weak transcription	K562	blood
14	chr1:151611600-151640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:151611600-151643800	Weak transcription	Pancreas	Pancrea
16	chr1:151611600-151668200	Weak transcription	Gastric	stomach
17	chr1:151612400-151634600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:151612800-151633800	Weak transcription	HSMM	muscle
19	chr1:151612800-151652400	Weak transcription	HMEC	breast
20	chr1:151618000-151642600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:151618000-151667600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151622800-151643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:151623000-151641600	Weak transcription	Ovary	ovary
24	chr1:151625000-151636600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:151625600-151644800	Strong transcription	Dnd41	blood
26	chr1:151626200-151636400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:151626800-151665400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:151627000-151634200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:151627200-151638200	Weak transcription	GM12878-XiMat	blood
30	chr1:151627200-151655600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:151627200-151659800	Weak transcription	Spleen	Spleen
32	chr1:151627200-151670600	Weak transcription	Small Intestine	intestine
33	chr1:151627400-151633000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:151627400-151638800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:151627400-151676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:151627600-151634600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:151627800-151634200	Weak transcription	Fetal Brain Female	brain
38	chr1:151628000-151646000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:151628200-151633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:151628200-151633600	Weak transcription	Primary T cells from cord blood	blood
41	chr1:151628200-151652800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:151628200-151669800	Weak transcription	Esophagus	oesophagus
43	chr1:151629000-151633800	Strong transcription	Fetal Intestine Large	intestine
44	chr1:151629000-151636600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:151629200-151643400	Weak transcription	Brain Substantia Nigra	brain
46	chr1:151629400-151637000	Strong transcription	HepG2	liver
47	chr1:151629600-151636600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:151629600-151642400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:151629800-151632800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:151629800-151636800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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