Variant report

Variant	rs1054475
Chromosome Location	chr1:151746235-151746236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:151746194-151746538	K562	blood:	n/a	n/a
2	FOS	chr1:151746166-151746613	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:151746193-151746552	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:151746166-151746627	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:151746202-151746584	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:151746160-151746628	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL1	chr1:151746123-151746611	HCT-116	colon:	n/a	n/a
8	MYC	chr1:151746220-151746524	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F4	chr1:151746223-151746485	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr1:151746161-151747594	K562	blood:	n/a	n/a
11	USF1	chr1:151746126-151746475	K562	blood:	n/a	n/a
12	STAT3	chr1:151746185-151746581	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:151746141-151746596	MCF10A-Er-Src	breast:	n/a	n/a
14	ATF1	chr1:151746222-151746523	K562	blood:	n/a	n/a
15	STAT3	chr1:151745960-151746539	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr1:151746174-151746569	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151734673..151739235-chr1:151743434..151748412,7	K562	blood:
2	chr1:151744411..151746345-chr1:151749411..151752360,2	K562	blood:
3	chr1:151744403..151747362-chr3:64316388..64318977,2	MCF-7	breast:
4	chr1:151743016..151748388-chr1:151755339..151760990,6	MCF-7	breast:
5	chr1:151737417..151739584-chr1:151745099..151746694,2	K562	blood:
6	chr1:151741435..151743883-chr1:151746073..151749758,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000249602	TF binding region
ENSG00000182134	Chromatin interaction
ENSG00000232937	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000268288	Chromatin interaction
ENSG00000249602	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1123855	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]
rs12748967	0.84[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[MEX][hapmap]
rs1623480	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1781421	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];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1781423	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781424	0.99[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];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996731	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996732	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460997	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2495396	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35077383	0.99[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	0.95[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	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4484926	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs4634911	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845339	0.81[CHB][hapmap]
rs4845355	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.90[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	0.81[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	0.84[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];0.95[CHB][hapmap];1.00[JPT][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]
rs6680404	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684101	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[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];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][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];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][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
rs1054475	TDRKH	cis	parietal	SCAN
rs1054475	BCL9	cis	cerebellum	SCAN
rs1054475	PLEKHO1	cis	cerebellum	SCAN
rs1054475	LYSMD1	cis	parietal	SCAN
rs1054475	TDRKH	cis	cerebellum	SCAN
rs1054475	CTSK	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736600-151746600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:151736600-151751000	Weak transcription	Ovary	ovary
3	chr1:151736800-151746400	Weak transcription	Aorta	Aorta
4	chr1:151736800-151746400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:151736800-151746400	Weak transcription	Right Ventricle	heart
6	chr1:151736800-151746600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:151736800-151746600	Weak transcription	Psoas Muscle	Psoas
8	chr1:151736800-151746800	Weak transcription	Left Ventricle	heart
9	chr1:151736800-151746800	Weak transcription	Spleen	Spleen
10	chr1:151736800-151747200	Weak transcription	Fetal Brain Male	brain
11	chr1:151736800-151747400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:151736800-151747800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:151736800-151748000	Weak transcription	Colonic Mucosa	Colon
14	chr1:151736800-151750800	Weak transcription	Right Atrium	heart
15	chr1:151736800-151762600	Weak transcription	Gastric	stomach
16	chr1:151737000-151746400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:151737000-151746400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:151737000-151746400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:151737000-151746400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:151737000-151746400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:151737000-151746400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:151737000-151746400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:151737000-151746400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:151737000-151746400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:151737000-151746600	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:151737000-151747400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:151737000-151747800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:151737000-151748000	Weak transcription	Fetal Stomach	stomach
29	chr1:151737000-151748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:151737000-151752200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:151737000-151762400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:151737000-151762400	Weak transcription	HSMMtube	muscle
33	chr1:151737000-151762600	Weak transcription	Small Intestine	intestine
34	chr1:151737200-151746400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:151737200-151746400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:151737200-151746400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:151737200-151748000	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:151737200-151753800	Weak transcription	A549	lung
39	chr1:151737800-151748400	Weak transcription	HepG2	liver
40	chr1:151738600-151750600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:151739400-151753200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:151740800-151747400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:151740800-151759000	Weak transcription	Esophagus	oesophagus
44	chr1:151741000-151747000	Weak transcription	Pancreas	Pancrea
45	chr1:151741000-151762600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:151741200-151746600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:151741200-151753000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:151741200-151756200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:151742400-151755200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:151742800-151762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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