Variant report

Variant	rs6587756
Chromosome Location	chr1:150546865-150546866
allele	A/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:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150545934..150547649-chr1:150567302..150569853,2	K562	blood:
2	chr1:150455770..150459652-chr1:150544183..150547234,4	K562	blood:
3	chr1:150543953..150547860-chr1:150600449..150605575,7	K562	blood:
4	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
5	chr1:150543938..150548482-chr1:150576509..150579510,5	K562	blood:
6	chr1:150545565..150549511-chr1:150783335..150787451,6	K562	blood:
7	chr1:150545938..150547543-chr1:150804208..150806124,2	K562	blood:
8	chr1:150544693..150547632-chr1:150583989..150587707,3	MCF-7	breast:
9	chr1:150544010..150546916-chr1:150590925..150592477,2	MCF-7	breast:
10	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
11	chr1:150545107..150547028-chr1:150615492..150618208,2	K562	blood:
12	chr1:150545938..150548404-chr1:150780767..150782416,2	K562	blood:
13	chr1:150545388..150547945-chr1:150570621..150572716,2	K562	blood:
14	chr1:150545613..150547144-chr1:150678229..150680325,2	K562	blood:
15	chr1:150435919..150438376-chr1:150544338..150547064,3	K562	blood:
16	chr1:150545560..150548928-chr1:150668482..150671179,4	K562	blood:
17	chr1:150545274..150547768-chr1:150592688..150595152,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf138-3	chr1:150546600-150547028	NR_104133

No data

Variant related genes	Relation type
ENSG00000143457	Chromatin interaction
ENSG00000143387	Chromatin interaction
ENSG00000143452	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10788792	0.95[CHB][hapmap]
rs10888391	0.87[CHB][hapmap]
rs11204666	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11204671	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204691	0.91[CHB][hapmap]
rs11204697	0.91[CHB][hapmap]
rs11204698	0.95[CHB][hapmap]
rs11204704	0.91[CHB][hapmap]
rs11204722	0.91[CHB][hapmap]
rs11204726	0.91[CHB][hapmap]
rs1136808	0.87[CHB][hapmap]
rs11586422	0.91[CHB][hapmap]
rs11587444	0.95[CHB][hapmap]
rs11803569	0.91[CHB][hapmap]
rs11803940	0.95[CHB][hapmap]
rs11804276	0.91[CHB][hapmap]
rs11807409	0.91[CHB][hapmap]
rs11807450	0.95[CHB][hapmap]
rs12063547	0.91[CHB][hapmap]
rs12072339	0.91[CHB][hapmap]
rs12086472	0.91[CHB][hapmap]
rs12089989	0.91[CHB][hapmap]
rs12402939	0.95[CHB][hapmap]
rs12403255	0.91[CHB][hapmap]
rs1336899	0.95[CHB][hapmap]
rs1336900	0.95[CHB][hapmap]
rs1415148	0.87[CHB][hapmap]
rs16827671	0.91[CHB][hapmap]
rs17658705	0.86[CHB][hapmap]
rs2184833	0.95[CHB][hapmap]
rs2275235	0.95[CHB][hapmap]
rs2275236	0.91[CHB][hapmap]
rs2280078	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2867301	0.91[CHB][hapmap]
rs2867302	0.91[CHB][hapmap]
rs35967040	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768005	0.95[CHB][hapmap]
rs3768018	0.87[CHB][hapmap]
rs4537557	0.95[CHB][hapmap]
rs6587516	0.91[CHB][hapmap]
rs6587518	0.91[CHB][hapmap]
rs6655975	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661415	0.91[CHB][hapmap]
rs6678013	0.91[CHB][hapmap]
rs6681426	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6695123	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6700022	0.95[CHB][hapmap]
rs7412396	0.87[CHB][hapmap]
rs7418501	0.91[CHB][hapmap]
rs7511673	0.95[CHB][hapmap]
rs7521898	0.95[CHB][hapmap]
rs7524620	0.91[CHB][hapmap]
rs7529194	0.95[CHB][hapmap]
rs7538493	0.91[CHB][hapmap]
rs7540874	0.91[CHB][hapmap]
rs7549723	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868751	0.95[CHB][hapmap]
rs951281	0.91[CHB][hapmap]

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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs6587756	GOLPH3L	cis	Nerve Tibial	GTEx
rs6587756	CTSS	cis	Lymphoblastoid	GTEx
rs6587756	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6587756	CTSS	cis	multi-tissue	Pritchard
rs6587756	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6587756	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6587756	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6587756	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6587756	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6587756	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs6587756	RP11-316M1.12	cis	Thyroid	GTEx
rs6587756	HORMAD1	cis	uninvolved skin	skin_eQTL
rs6587756	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6587756	HORMAD1	cis	normal skin	skin_eQTL
rs6587756	HORMAD1	cis	lesional skin	skin_eQTL
rs6587756	RP11-316M1.12	cis	lung	GTEx
rs6587756	CTSS	cis	Thyroid	GTEx
rs6587756	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs6587756	RP11-316M1.12	cis	Whole Blood	GTEx
rs6587756	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6587756	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6587756	HORMAD1	cis	Nerve Tibial	GTEx
rs6587756	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6587756	RP11-316M1.12	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150541400-150547200	Genic enhancers	Fetal Intestine Small	intestine
3	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:150542000-150547200	Genic enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:150542200-150547200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:150542200-150547200	Strong transcription	Brain Germinal Matrix	brain
7	chr1:150542200-150548000	Genic enhancers	Placenta	Placenta
8	chr1:150542400-150547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:150542600-150547200	Genic enhancers	Lung	lung
10	chr1:150542600-150548200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:150542800-150547800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:150542800-150551600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
13	chr1:150543000-150549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:150543200-150547000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:150543400-150547000	Genic enhancers	Osteobl	bone
16	chr1:150543600-150547200	Genic enhancers	Dnd41	blood
17	chr1:150543600-150547800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:150543600-150548200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
21	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:150543800-150547000	Strong transcription	Fetal Lung	lung
23	chr1:150544000-150547000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:150544000-150547200	Strong transcription	Fetal Stomach	stomach
25	chr1:150544000-150547400	Weak transcription	Fetal Brain Male	brain
26	chr1:150544200-150551600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
27	chr1:150544400-150547200	Genic enhancers	Fetal Intestine Large	intestine
28	chr1:150544600-150551600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
29	chr1:150544800-150547000	Genic enhancers	Left Ventricle	heart
30	chr1:150544800-150548400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:150545000-150547200	Genic enhancers	A549	lung
32	chr1:150545000-150548600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:150545000-150550000	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
34	chr1:150545000-150551400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
35	chr1:150545200-150547000	Genic enhancers	Hela-S3	cervix
36	chr1:150545200-150547200	Genic enhancers	Brain Anterior Caudate	brain
37	chr1:150545200-150547200	Genic enhancers	NHDF-Ad	bronchial
38	chr1:150545200-150547400	Genic enhancers	HepG2	liver
39	chr1:150545200-150548400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:150545200-150550200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:150545200-150551000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
42	chr1:150545200-150551000	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
43	chr1:150545200-150551400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:150545200-150551400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:150545200-150551600	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
46	chr1:150545200-150552000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
47	chr1:150545400-150547000	Genic enhancers	Primary hematopoietic stem cells	blood
48	chr1:150545400-150547200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
49	chr1:150545400-150547400	Genic enhancers	Stomach Mucosa	stomach
50	chr1:150545400-150551000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood

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