Variant report

Variant	rs7540530
Chromosome Location	chr1:151790858-151790859
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: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	chr1:151779245..151781251-chr1:151789971..151792071,2	K562	blood:
2	chr1:151749151..151752129-chr1:151789791..151791884,2	MCF-7	breast:
3	chr1:151777634..151779857-chr1:151790173..151792393,2	MCF-7	breast:
4	chr1:151789315..151792282-chr1:151793123..151796667,3	MCF-7	breast:
5	chr1:151789798..151791316-chr1:151791321..151793300,2	MCF-7	breast:
6	chr1:151789925..151792025-chr1:151796878..151798485,2	K562	blood:
7	chr1:151768081..151769884-chr1:151790238..151792555,2	MCF-7	breast:
8	chr1:151789037..151791366-chr1:151802324..151804335,2	K562	blood:
9	chr1:151778487..151781437-chr1:151789485..151791157,2	K562	blood:
10	chr1:151782377..151784450-chr1:151790300..151792878,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143365	Chromatin interaction
ENSG00000213171	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11204895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036145	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144914	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587620	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540027	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540034	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv160848	chr1:151789609-151796769	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7540530	GABPB2	cis	parietal	SCAN
rs7540530	HRNR	cis	cerebellum	SCAN
rs7540530	LCE3D	cis	cerebellum	SCAN
rs7540530	MTMR11	cis	cerebellum	SCAN
rs7540530	S100A10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151792800	Weak transcription	Lung	lung
2	chr1:151778400-151792800	Weak transcription	Left Ventricle	heart
3	chr1:151778600-151792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:151778600-151802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:151780000-151793400	Weak transcription	Stomach Mucosa	stomach
6	chr1:151782000-151791000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:151783600-151791400	Weak transcription	Hela-S3	cervix
8	chr1:151783800-151792000	Weak transcription	Psoas Muscle	Psoas
9	chr1:151784800-151794600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:151784800-151794800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:151786600-151791000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:151786600-151793600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:151786800-151793600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:151786800-151795000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:151787000-151791600	Enhancers	Fetal Muscle Leg	muscle
16	chr1:151787400-151800000	Weak transcription	Spleen	Spleen
17	chr1:151787600-151791000	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:151788200-151793200	Transcr. at gene 5' and 3'	Thymus	Thymus
19	chr1:151788200-151796800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
20	chr1:151788800-151792200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:151789000-151791000	Enhancers	Esophagus	oesophagus
22	chr1:151789000-151792000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:151789000-151792400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:151789000-151793000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:151789400-151791600	Genic enhancers	Liver	Liver
26	chr1:151789400-151794400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:151789400-151794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:151789600-151792000	Weak transcription	Gastric	stomach
29	chr1:151789600-151792400	Weak transcription	Right Ventricle	heart
30	chr1:151789600-151793600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:151790000-151792800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:151790000-151793200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:151790000-151799000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:151790200-151792400	Weak transcription	Primary T cells from cord blood	blood
35	chr1:151790200-151792400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:151790200-151792400	Weak transcription	Adipose Nuclei	Adipose
37	chr1:151790200-151793000	Weak transcription	GM12878-XiMat	blood
38	chr1:151790200-151793200	Weak transcription	Fetal Intestine Large	intestine
39	chr1:151790200-151801600	Weak transcription	Right Atrium	heart
40	chr1:151790400-151791600	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:151790400-151792200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:151790400-151792400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:151790400-151792400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:151790600-151791000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:151790600-151791400	Enhancers	Dnd41	blood
46	chr1:151790600-151792400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:151790600-151793800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:151790600-151794200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr1:151790800-151792000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:151790800-151792200	Genic enhancers	Pancreas	Pancrea

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