Variant report

Variant	rs11204725
Chromosome Location	chr1:150742700-150742701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150741916..150744860-chr1:150749050..150751954,2	K562	blood:
2	chr1:150738126..150741415-chr1:150742001..150744824,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163131	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 39 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1081512	0.81[EUR][1000 genomes]
rs10888388	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11204684	0.80[MKK][hapmap]
rs11204693	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs11204695	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap]
rs11204702	0.83[AFR][1000 genomes]
rs11204712	0.82[ASN][1000 genomes]
rs11204735	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs11204737	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs1136774	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125650	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126004	0.81[EUR][1000 genomes]
rs12130363	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12402006	0.80[EUR][1000 genomes]
rs12403609	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12404199	0.80[EUR][1000 genomes]
rs12410050	0.81[EUR][1000 genomes]
rs12568757	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12725806	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12758227	0.85[EUR][1000 genomes]
rs16841689	0.82[YRI][hapmap]
rs17599629	0.91[YRI][hapmap]
rs2039590	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2089081	0.88[EUR][1000 genomes]
rs34002273	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486836	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs4970924	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs4970926	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs4970976	0.85[EUR][1000 genomes]
rs6587520	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6694531	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7520022	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs7534124	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9733	0.88[ASW][hapmap];0.85[CEU][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872417	chr1:150618632-150759979	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1008381	chr1:150721254-150745558	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:39)

SNP	Gene	Cis/trans	Tissue	Source
rs11204725	ARNT	cis	uninvolved skin	skin_eQTL
rs11204725	CTSS	cis	multi-tissue	Pritchard
rs11204725	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204725	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11204725	CTSS	cis	cerebellum	SCAN
rs11204725	FMO5	cis	cerebellum	SCAN
rs11204725	ARNT	cis	normal skin	skin_eQTL
rs11204725	ARNT	cis	lesional skin	skin_eQTL
rs11204725	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204725	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204725	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204725	HORMAD1	cis	uninvolved skin	skin_eQTL
rs11204725	HORMAD1	cis	lesional skin	skin_eQTL
rs11204725	CTSS	cis	parietal	SCAN
rs11204725	CTSK	cis	parietal	SCAN
rs11204725	HORMAD1	cis	Nerve Tibial	GTEx
rs11204725	PSMD4	cis	parietal	SCAN
rs11204725	MCL1	cis	cerebellum	SCAN
rs11204725	RP11-316M1.12	cis	Thyroid	GTEx
rs11204725	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204725	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11204725	CTSS	cis	lymphoblastoid	seeQTL
rs11204725	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204725	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204725	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204725	ARNT	cis	multi-tissue	Pritchard
rs11204725	RP11-316M1.12	cis	Whole Blood	GTEx
rs11204725	CTSK	cis	multi-tissue	Pritchard
rs11204725	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs11204725	ARNT	cis	parietal	SCAN
rs11204725	RP11-316M1.12	cis	lung	GTEx
rs11204725	CTSK	cis	cerebellum	SCAN
rs11204725	HORMAD1	cis	parietal	SCAN
rs11204725	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11204725	CTSS	cis	Thyroid	GTEx
rs11204725	CTSK	cis	lymphoblastoid	seeQTL
rs11204725	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11204725	MLLT11	cis	lymphoblastoid	seeQTL
rs11204725	ARNT	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150737200-150761800	Weak transcription	Spleen	Spleen
2	chr1:150738600-150743200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:150738600-150743200	Weak transcription	Thymus	Thymus
4	chr1:150738800-150742800	Weak transcription	Fetal Thymus	thymus
5	chr1:150738800-150743000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:150738800-150743000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:150738800-150743000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:150738800-150743200	Weak transcription	Primary T cells from cord blood	blood
9	chr1:150738800-150743200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:150738800-150743200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:150738800-150743200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:150738800-150743200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:150738800-150743200	Weak transcription	Dnd41	blood
14	chr1:150738800-150743400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:150739000-150743200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:150739000-150743200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:150739000-150743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:150739200-150743000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:150739200-150743400	Weak transcription	Primary B cells from cord blood	blood
20	chr1:150739400-150742800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:150740600-150743000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr1:150740600-150743200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:150740800-150743000	Weak transcription	GM12878-XiMat	blood
24	chr1:150741600-150743200	Enhancers	Primary neutrophils fromperipheralblood	blood

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