Variant report

Variant	rs878471
Chromosome Location	chr1:150547747-150547748
allele	A/G
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150547190..150548914-chr1:150945735..150947586,2	MCF-7	breast:
2	chr1:150546983..150547940-chr5:96038144..96038846,2	Hela-S3	cervix:
3	chr1:150547449..150549825-chr1:150944265..150946222,2	K562	blood:
4	chr1:150547107..150548071-chr17:2302580..2303108,2	Hela-S3	cervix:
5	chr1:150543953..150547860-chr1:150600449..150605575,7	K562	blood:
6	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
7	chr1:150543938..150548482-chr1:150576509..150579510,5	K562	blood:
8	chr1:150547135..150548090-chr19:12903504..12904460,2	Hela-S3	cervix:
9	chr1:150545565..150549511-chr1:150783335..150787451,6	K562	blood:
10	chr1:150547577..150553391-chr1:150562900..150573800,12	MCF-7	breast:
11	chr1:150546929..150549035-chr1:150943072..150945219,2	MCF-7	breast:
12	chr1:150547666..150549235-chr1:150978267..150981074,2	MCF-7	breast:
13	chr1:150545938..150548404-chr1:150780767..150782416,2	K562	blood:
14	chr1:150545388..150547945-chr1:150570621..150572716,2	K562	blood:
15	chr1:150547675..150548533-chr3:128997621..128998212,2	Hela-S3	cervix:
16	chr1:150546941..150549825-chr1:150944265..150946222,3	K562	blood:
17	chr1:150547171..150547907-chr17:73716745..73717607,2	Hela-S3	cervix:
18	chr1:150547323..150548024-chr5:40835254..40836048,2	Hela-S3	cervix:
19	chr1:150545560..150548928-chr1:150668482..150671179,4	K562	blood:
20	chr1:150545274..150547768-chr1:150592688..150595152,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143418	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000183624	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000132470	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143387	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000153113	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10888384	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888385	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204668	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204669	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11204675	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204677	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11204678	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204679	0.92[ASN][1000 genomes]
rs11204680	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11204684	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs11585169	0.92[ASN][1000 genomes]
rs12116492	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12125672	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12126271	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139563	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12406712	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12746899	0.92[ASN][1000 genomes]
rs1971378	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs2048558	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3738484	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738485	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754209	0.81[ASN][1000 genomes]
rs4970918	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970923	0.81[ASN][1000 genomes]
rs4971041	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55862611	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61820165	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669122	0.81[ASN][1000 genomes]
rs6697620	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698495	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs932054	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9803935	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs878471	HORMAD1	cis	Esophagus Mucosa	GTEx
rs878471	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs878471	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs878471	ENSA	Cis_1M	lymphoblastoid	RTeQTL
rs878471	ARNT	cis	Thyroid	GTEx
rs878471	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs878471	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs878471	GOLPH3L	cis	Nerve Tibial	GTEx
rs878471	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs878471	HORMAD1	cis	uninvolved skin	skin_eQTL
rs878471	HORMAD1	cis	lesional skin	skin_eQTL
rs878471	HORMAD1	cis	normal skin	skin_eQTL
rs878471	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs878471	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs878471	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs878471	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:150542200-150548000	Genic enhancers	Placenta	Placenta
3	chr1:150542600-150548200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:150542800-150547800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:150542800-150551600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
6	chr1:150543000-150549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:150543600-150547800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:150543600-150548200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
11	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:150544200-150551600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
13	chr1:150544600-150551600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
14	chr1:150544800-150548400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:150545000-150548600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:150545000-150550000	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
17	chr1:150545000-150551400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
18	chr1:150545200-150548400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:150545200-150550200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:150545200-150551000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
21	chr1:150545200-150551000	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
22	chr1:150545200-150551400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:150545200-150551400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:150545200-150551600	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
25	chr1:150545200-150552000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
26	chr1:150545400-150551000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
27	chr1:150545400-150551000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
28	chr1:150545400-150551400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:150545400-150551600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
30	chr1:150545400-150551600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:150545600-150548000	Genic enhancers	H1 Cell Line	embryonic stem cell
32	chr1:150545600-150548000	Genic enhancers	K562	blood
33	chr1:150545600-150548400	Genic enhancers	Spleen	Spleen
34	chr1:150545600-150549200	Genic enhancers	Placenta Amnion	Placenta Amnion
35	chr1:150545600-150550200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
36	chr1:150545600-150551400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
37	chr1:150545600-150551400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
38	chr1:150546400-150547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:150546400-150548000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:150546800-150548600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
41	chr1:150546800-150548800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
42	chr1:150546800-150548800	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
43	chr1:150546800-150549000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
44	chr1:150546800-150550000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
45	chr1:150546800-150550400	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:150546800-150550400	Transcr. at gene 5' and 3'	HSMMtube	muscle
47	chr1:150546800-150551000	Transcr. at gene 5' and 3'	HMEC	breast
48	chr1:150546800-150551000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
49	chr1:150546800-150551200	Transcr. at gene 5' and 3'	NH-A	brain
50	chr1:150546800-150551400	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell

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