Variant report

Variant	rs6698495
Chromosome Location	chr1:150564476-150564477
allele	C/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150547577..150553391-chr1:150562900..150573800,12	MCF-7	breast:
2	chr1:150547964..150550614-chr1:150563444..150566002,2	K562	blood:
3	chr1:150554954..150558805-chr1:150562851..150567781,4	K562	blood:
4	chr1:150562742..150565276-chr1:150576021..150578249,2	K562	blood:
5	chr1:150549380..150556585-chr1:150561290..150565762,10	K562	blood:
6	chr1:150562735..150566350-chr1:150574658..150578740,6	K562	blood:
7	chr1:150550714..150554417-chr1:150561290..150565440,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1053732	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888384	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10888385	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204668	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204669	0.89[ASN][1000 genomes]
rs11204675	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204676	0.83[AFR][1000 genomes]
rs11204677	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204678	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204679	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204680	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]
rs11204684	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204693	0.81[CHD][hapmap]
rs11585169	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12116492	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12125672	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126271	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12139563	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12406712	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12746899	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971378	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2048558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738484	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3738485	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754209	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4970918	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970923	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971041	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs55862611	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61820165	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6669122	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697620	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878471	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs932054	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9803935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs6698495	PSMD4	cis	parietal	SCAN
rs6698495	GOLPH3L	cis	Nerve Tibial	GTEx
rs6698495	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6698495	TXNIP	cis	parietal	SCAN
rs6698495	CTSK	cis	cerebellum	SCAN
rs6698495	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6698495	CTSS	cis	parietal	SCAN
rs6698495	ARNT	cis	normal skin	skin_eQTL
rs6698495	HORMAD1	cis	uninvolved skin	skin_eQTL
rs6698495	ARNT	cis	parietal	SCAN
rs6698495	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6698495	HORMAD1	cis	Nerve Tibial	GTEx
rs6698495	MCL1	cis	cerebellum	SCAN
rs6698495	CTSS	cis	Nerve Tibial	GTEx
rs6698495	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6698495	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6698495	HORMAD1	cis	normal skin	skin_eQTL
rs6698495	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6698495	POLR3GL	cis	cerebellum	SCAN
rs6698495	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6698495	CTSK	cis	parietal	SCAN
rs6698495	ARNT	cis	cerebellum	SCAN
rs6698495	ARNT	cis	Thyroid	GTEx
rs6698495	CTSS	cis	cerebellum	SCAN
rs6698495	HORMAD1	cis	parietal	SCAN
rs6698495	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6698495	FMO5	cis	cerebellum	SCAN
rs6698495	HORMAD1	cis	lesional skin	skin_eQTL
rs6698495	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6698495	TCHHL1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150572800	Weak transcription	Thymus	Thymus
2	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:150553200-150566000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:150553200-150568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:150553200-150569400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:150553200-150569400	Weak transcription	Fetal Thymus	thymus
7	chr1:150553200-150572600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:150553200-150572600	Weak transcription	Fetal Brain Female	brain
9	chr1:150553200-150572800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:150553200-150577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:150553200-150581800	Weak transcription	Dnd41	blood
13	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
15	chr1:150553800-150568000	Weak transcription	HSMM	muscle
16	chr1:150553800-150572600	Weak transcription	Lung	lung
17	chr1:150553800-150576800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:150554000-150568400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:150554000-150568600	Weak transcription	Hela-S3	cervix
20	chr1:150554000-150572000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:150554200-150568400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:150554400-150572600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:150555400-150568400	Weak transcription	Osteobl	bone
25	chr1:150555400-150572600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
27	chr1:150555600-150568400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:150555600-150568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:150556000-150564800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:150557200-150568400	Weak transcription	Fetal Intestine Small	intestine
31	chr1:150558800-150568400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:150560200-150576000	Weak transcription	Ovary	ovary
33	chr1:150561200-150565800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:150561200-150572400	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:150561400-150577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:150561800-150581800	Weak transcription	Brain Substantia Nigra	brain
37	chr1:150562200-150583200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:150563000-150572400	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:150563000-150583800	Weak transcription	Fetal Lung	lung
40	chr1:150564000-150566200	Strong transcription	Fetal Stomach	stomach
41	chr1:150564000-150576200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:150564400-150565600	Enhancers	Placenta	Placenta
43	chr1:150564400-150566000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:150564400-150583800	Weak transcription	Rectal Mucosa Donor 29	rectum

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