Variant report

Variant	rs6587520
Chromosome Location	chr1:150709723-150709724
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	chr1:150693906..150695724-chr1:150707796..150710727,2	K562	blood:
2	chr1:150692737..150694366-chr1:150708966..150711892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143452	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10888388	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204693	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204695	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204702	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204712	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204725	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1136774	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11800059	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12125650	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12130363	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12403609	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568757	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34002273	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4970924	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970926	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694531	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7520022	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534124	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]

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	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	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
3	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
4	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
5	nsv872419	chr1:150699199-150738759	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6587520	ARNT	cis	Thyroid	GTEx
rs6587520	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6587520	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6587520	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs6587520	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6587520	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6587520	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6587520	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6587520	RP11-316M1.12	cis	Artery Tibial	GTEx
rs6587520	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6587520	RP11-316M1.12	cis	Whole Blood	GTEx
rs6587520	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6587520	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6587520	RP11-316M1.12	cis	Thyroid	GTEx
rs6587520	GOLPH3L	cis	Nerve Tibial	GTEx
rs6587520	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6587520	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6587520	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150701400-150710000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:150701400-150727400	Weak transcription	Left Ventricle	heart
3	chr1:150701800-150710400	Weak transcription	Adipose Nuclei	Adipose
4	chr1:150702400-150716200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:150702600-150715800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:150702600-150716200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:150702600-150716200	Strong transcription	Primary B cells from cord blood	blood
8	chr1:150702600-150716200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:150702800-150716200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:150703200-150713200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:150703800-150717200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:150704000-150711600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:150704000-150715800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:150704000-150716200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:150704000-150716200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:150704000-150736600	Weak transcription	Fetal Stomach	stomach
17	chr1:150704200-150716200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:150704400-150716200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:150704400-150716200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:150704400-150716200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:150704400-150716200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:150704400-150716200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr1:150704600-150715800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:150704600-150717400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:150704800-150715000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:150704800-150715200	Weak transcription	Small Intestine	intestine
27	chr1:150705400-150723800	Weak transcription	Gastric	stomach
28	chr1:150705600-150723800	Weak transcription	Thymus	Thymus
29	chr1:150706000-150710200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:150706000-150712200	Weak transcription	Colonic Mucosa	Colon
31	chr1:150706200-150709800	Weak transcription	GM12878-XiMat	blood
32	chr1:150706600-150710400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:150707000-150716200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:150707200-150715800	Strong transcription	Primary T cells from cord blood	blood
35	chr1:150707600-150713200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:150707600-150715800	Strong transcription	Liver	Liver
37	chr1:150708000-150711400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:150708200-150710000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:150708200-150710200	Weak transcription	Spleen	Spleen
40	chr1:150708400-150733000	Weak transcription	Fetal Intestine Large	intestine
41	chr1:150709000-150710800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:150709000-150719000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:150709000-150723800	Weak transcription	Esophagus	oesophagus
44	chr1:150709000-150727400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:150709400-150714000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:150709600-150712000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:150709600-150713600	Strong transcription	Lung	lung
48	chr1:150709600-150713800	Strong transcription	Fetal Thymus	thymus

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