Variant report

Variant	rs1123855
Chromosome Location	chr1:151747043-151747044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151734673..151739235-chr1:151743434..151748412,7	K562	blood:
2	chr1:151744403..151747362-chr3:64316388..64318977,2	MCF-7	breast:
3	chr1:151743016..151748388-chr1:151755339..151760990,6	MCF-7	breast:
4	chr1:151741435..151743883-chr1:151746073..151749758,4	K562	blood:

Variant related genes	Relation type
ENSG00000182134	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000249602	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000232937	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1054475	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586691	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11806815	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12143606	0.83[CHB][hapmap]
rs12748967	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12756855	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758387	0.85[CHB][hapmap];0.81[MEX][hapmap]
rs1623480	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1781421	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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1781423	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915544	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996731	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996732	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2495396	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35077383	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35834074	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828057	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs3923394	0.81[GIH][hapmap]
rs4240870	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4484926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845339	0.88[CHB][hapmap]
rs4845355	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845556	0.98[EUR][1000 genomes]
rs4995159	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55982513	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60136317	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61815091	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61815098	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61815099	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587619	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680404	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684101	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521817	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7523001	0.85[EUR][1000 genomes]
rs7529549	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868866	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs868867	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1123855	LYSMD1	cis	parietal	SCAN
rs1123855	CTSK	cis	cerebellum	SCAN
rs1123855	TDRKH	cis	cerebellum	SCAN
rs1123855	TDRKH	cis	parietal	SCAN
rs1123855	PLEKHO1	cis	cerebellum	SCAN
rs1123855	BCL9	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736600-151751000	Weak transcription	Ovary	ovary
2	chr1:151736800-151747200	Weak transcription	Fetal Brain Male	brain
3	chr1:151736800-151747400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:151736800-151747800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:151736800-151748000	Weak transcription	Colonic Mucosa	Colon
6	chr1:151736800-151750800	Weak transcription	Right Atrium	heart
7	chr1:151736800-151762600	Weak transcription	Gastric	stomach
8	chr1:151737000-151747400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:151737000-151747800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:151737000-151748000	Weak transcription	Fetal Stomach	stomach
11	chr1:151737000-151748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:151737000-151752200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:151737000-151762400	Weak transcription	Fetal Intestine Small	intestine
14	chr1:151737000-151762400	Weak transcription	HSMMtube	muscle
15	chr1:151737000-151762600	Weak transcription	Small Intestine	intestine
16	chr1:151737200-151748000	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:151737200-151753800	Weak transcription	A549	lung
18	chr1:151737800-151748400	Weak transcription	HepG2	liver
19	chr1:151738600-151750600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:151739400-151753200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:151740800-151747400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:151740800-151759000	Weak transcription	Esophagus	oesophagus
23	chr1:151741000-151762600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:151741200-151753000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:151741200-151756200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:151742400-151755200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:151742800-151762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:151744000-151762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:151744200-151750600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:151744600-151762200	Weak transcription	Primary B cells from cord blood	blood
31	chr1:151745200-151752600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:151745200-151752800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:151745400-151749800	Strong transcription	Fetal Brain Female	brain
34	chr1:151745400-151753200	Weak transcription	Fetal Kidney	kidney
35	chr1:151745400-151755600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:151745600-151754400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:151745600-151755400	Strong transcription	Primary T cells from cord blood	blood
38	chr1:151745800-151747200	Enhancers	HMEC	breast
39	chr1:151745800-151747400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:151745800-151748200	Strong transcription	Liver	Liver
41	chr1:151745800-151749400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:151745800-151752800	Strong transcription	Brain Substantia Nigra	brain
43	chr1:151745800-151754600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:151745800-151754600	Strong transcription	Brain Germinal Matrix	brain
45	chr1:151745800-151755000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:151745800-151755400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:151745800-151755600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:151745800-151755600	Strong transcription	Dnd41	blood
49	chr1:151746000-151748000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:151746000-151748000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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