Variant report

Variant	rs11204680
Chromosome Location	chr1:150587140-150587141
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150543642..150545689-chr1:150586263..150588774,2	MCF-7	breast:
2	chr1:150575575..150579360-chr1:150586267..150590184,5	MCF-7	breast:
3	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
4	chr1:150540599..150543052-chr1:150586269..150588685,3	K562	blood:
5	chr1:150544693..150547632-chr1:150583989..150587707,3	MCF-7	breast:
6	chr1:150575574..150579805-chr1:150584520..150587966,8	K562	blood:
7	chr1:150583951..150586668-chr1:150586711..150588335,2	K562	blood:
8	chr1:150516867..150518904-chr1:150586096..150587673,2	K562	blood:
9	chr1:150532483..150534415-chr1:150583903..150587502,3	K562	blood:
10	chr1:150544073..150554289-chr1:150582699..150598712,61	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction
ENSG00000264584	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000264508	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 31 )

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

rs_ID	r²[population]
rs1053732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888384	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888385	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204668	0.89[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204669	0.87[ASN][1000 genomes]
rs11204675	0.85[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204677	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204678	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204684	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204693	0.83[CHD][hapmap]
rs11204695	0.81[CHD][hapmap]
rs11585169	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12116492	0.89[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12125672	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126271	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12139563	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12406712	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12568757	0.81[CHD][hapmap]
rs12746899	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971378	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048558	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738484	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738485	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754209	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970918	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970923	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970924	0.81[CHD][hapmap]
rs4970926	0.81[CHD][hapmap]
rs4971041	0.89[ASW][hapmap];0.82[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55862611	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61820165	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669122	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6694531	0.81[CHD][hapmap]
rs6697620	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698495	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520022	0.81[CHD][hapmap]
rs878471	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs932054	0.85[ASN][1000 genomes]
rs9803935	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs11204680	PSMD4	cis	parietal	SCAN
rs11204680	ARNT	cis	normal skin	skin_eQTL
rs11204680	MCL1	cis	cerebellum	SCAN
rs11204680	GOLPH3L	cis	Nerve Tibial	GTEx
rs11204680	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204680	HORMAD1	cis	parietal	SCAN
rs11204680	CTSK	cis	lymphoblastoid	seeQTL
rs11204680	ARNT	cis	cerebellum	SCAN
rs11204680	CTSK	cis	parietal	SCAN
rs11204680	CTSS	cis	cerebellum	SCAN
rs11204680	HORMAD1	cis	Nerve Tibial	GTEx
rs11204680	ARNT	cis	parietal	SCAN
rs11204680	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204680	HORMAD1	cis	normal skin	skin_eQTL
rs11204680	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204680	HORMAD1	cis	lesional skin	skin_eQTL
rs11204680	POLR3GL	cis	cerebellum	SCAN
rs11204680	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204680	CTSK	cis	cerebellum	SCAN
rs11204680	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204680	FMO5	cis	cerebellum	SCAN
rs11204680	HORMAD1	cis	uninvolved skin	skin_eQTL
rs11204680	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204680	CTSS	cis	parietal	SCAN
rs11204680	ARNT	cis	Thyroid	GTEx
rs11204680	TXNIP	cis	parietal	SCAN
rs11204680	TCHHL1	cis	parietal	SCAN
rs11204680	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11204680	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204680	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204680	CTSS	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
2	chr1:150573400-150587800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:150576200-150591000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:150577000-150588400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:150577400-150587800	Weak transcription	Esophagus	oesophagus
6	chr1:150578000-150592600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:150582200-150587800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:150582200-150588800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:150582400-150588800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:150582400-150594400	Weak transcription	Ovary	ovary
11	chr1:150582600-150591800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:150582800-150587800	Weak transcription	Fetal Brain Male	brain
13	chr1:150583000-150587600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:150583000-150588000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr1:150583200-150588000	Genic enhancers	Fetal Intestine Small	intestine
16	chr1:150583200-150589000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:150583400-150588200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:150583600-150588000	Enhancers	Liver	Liver
19	chr1:150584000-150588600	Strong transcription	Fetal Brain Female	brain
20	chr1:150584200-150587600	Weak transcription	Fetal Lung	lung
21	chr1:150584400-150588600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:150584400-150594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:150584400-150600600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:150584600-150588200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:150584600-150589400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:150584800-150587200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:150584800-150587600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:150584800-150587600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:150584800-150587800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:150584800-150589600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:150584800-150591400	Weak transcription	Right Ventricle	heart
32	chr1:150584800-150591600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:150584800-150594400	Weak transcription	Gastric	stomach
34	chr1:150584800-150596200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:150584800-150600200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:150585000-150600000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:150585200-150600200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:150585400-150587200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:150585400-150588000	Enhancers	Stomach Mucosa	stomach
40	chr1:150585400-150594200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:150585600-150587200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:150585600-150587200	Enhancers	Fetal Intestine Large	intestine
43	chr1:150585600-150588800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr1:150585600-150589200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:150585600-150589200	Enhancers	Small Intestine	intestine
46	chr1:150585600-150591600	Weak transcription	Psoas Muscle	Psoas
47	chr1:150585800-150587200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:150585800-150588000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:150586000-150587600	Strong transcription	Fetal Thymus	thymus
50	chr1:150586000-150587800	Weak transcription	Thymus	Thymus

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