Variant report

Variant	rs11575510
Chromosome Location	chr7:50536168-50536169
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:50535831..50536349-chr7:50746766..50747605,2	K562	blood:
2	chr7:50534464..50537080-chr7:50740963..50742721,2	K562	blood:
3	chr7:50535510..50536363-chr7:50662884..50663430,2	MCF-7	breast:
4	chr7:50535864..50536412-chr7:50746634..50747334,2	MCF-7	breast:
5	chr7:50530045..50531842-chr7:50534711..50537256,2	K562	blood:
6	chr7:50535443..50536367-chr7:50700303..50701436,9	MCF-7	breast:
7	chr7:50535360..50536453-chr7:51227965..51229366,4	K562	blood:
8	chr7:50535602..50536304-chr7:50700570..50701281,2	K562	blood:
9	chr7:50535593..50536314-chr7:50677309..50677832,2	MCF-7	breast:

No data

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10499693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575293	1.00[EUR][1000 genomes]
rs11575302	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575340	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575343	1.00[EUR][1000 genomes]
rs11575360	1.00[EUR][1000 genomes]
rs11575381	1.00[EUR][1000 genomes]
rs11575385	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575407	1.00[EUR][1000 genomes]
rs11575447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575493	1.00[EUR][1000 genomes]
rs11575494	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575502	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575503	1.00[EUR][1000 genomes]
rs11575504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575505	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575507	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575514	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575519	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575531	0.82[AFR][1000 genomes]
rs11575535	0.90[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11575537	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575540	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575542	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575546	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575547	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575549	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11978797	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11981575	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11982708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11982772	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11982776	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11983581	1.00[CEU][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11983757	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12112308	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12113897	0.84[EUR][1000 genomes]
rs2329370	1.00[EUR][1000 genomes]
rs3173669	0.92[EUR][1000 genomes]
rs55869201	1.00[EUR][1000 genomes]
rs55992615	1.00[EUR][1000 genomes]
rs56030652	1.00[EUR][1000 genomes]
rs57167849	0.92[EUR][1000 genomes]
rs57835901	1.00[EUR][1000 genomes]
rs59150746	1.00[EUR][1000 genomes]
rs59828622	0.92[EUR][1000 genomes]
rs6956737	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6975312	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6978556	0.92[EUR][1000 genomes]
rs73695512	1.00[EUR][1000 genomes]
rs73695638	0.84[EUR][1000 genomes]
rs73695639	0.92[EUR][1000 genomes]
rs73695640	0.92[EUR][1000 genomes]
rs73695641	0.92[EUR][1000 genomes]
rs73695643	0.92[EUR][1000 genomes]
rs73695661	0.92[EUR][1000 genomes]
rs73695664	0.92[EUR][1000 genomes]
rs73695666	0.92[EUR][1000 genomes]
rs73695667	0.92[EUR][1000 genomes]
rs73695668	0.92[EUR][1000 genomes]
rs73695669	0.92[EUR][1000 genomes]
rs73695670	0.92[EUR][1000 genomes]
rs73695671	0.92[EUR][1000 genomes]
rs73695672	0.92[EUR][1000 genomes]
rs73695673	0.92[EUR][1000 genomes]
rs73695681	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695683	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695700	1.00[EUR][1000 genomes]
rs73695701	1.00[EUR][1000 genomes]
rs73695702	1.00[EUR][1000 genomes]
rs73697528	1.00[EUR][1000 genomes]
rs73697574	1.00[EUR][1000 genomes]
rs930707	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9942578	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1026081	chr7:50525900-50538184	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11575510	PGAM2	trans	brain	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535200-50536200	Enhancers	Fetal Brain Male	brain
2	chr7:50535200-50536400	Enhancers	Fetal Thymus	thymus
3	chr7:50535400-50536200	Enhancers	Primary hematopoietic stem cells	blood
4	chr7:50535400-50536200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:50535400-50536200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr7:50535400-50536200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr7:50535400-50536200	Genic enhancers	Fetal Intestine Small	intestine
8	chr7:50535400-50536400	Enhancers	Primary B cells from peripheral blood	blood
9	chr7:50535400-50536400	Enhancers	Primary T cells from cord blood	blood
10	chr7:50535400-50536400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:50535400-50536400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:50535400-50536400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:50535400-50536400	Bivalent Enhancer	Fetal Stomach	stomach
14	chr7:50535400-50536400	Enhancers	Thymus	Thymus
15	chr7:50535400-50536600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:50535600-50536200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:50535600-50536200	Enhancers	Primary B cells from cord blood	blood
18	chr7:50535600-50536200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr7:50535600-50536200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:50535600-50536200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:50535600-50536200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:50535600-50536200	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr7:50535600-50536200	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr7:50535600-50536200	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr7:50535600-50536200	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr7:50535600-50536200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr7:50535600-50536200	Enhancers	Fetal Lung	lung
28	chr7:50535600-50536200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr7:50535600-50536200	Genic enhancers	Right Atrium	heart
30	chr7:50535600-50536200	Enhancers	HepG2	liver
31	chr7:50535600-50536400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr7:50535600-50536400	Enhancers	Colon Smooth Muscle	Colon
33	chr7:50535600-50536400	Genic enhancers	Fetal Intestine Large	intestine
34	chr7:50535600-50536600	Enhancers	Esophagus	oesophagus
35	chr7:50535800-50536200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
36	chr7:50535800-50536200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr7:50535800-50536200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:50535800-50536200	Flanking Bivalent TSS/Enh	Dnd41	blood
39	chr7:50535800-50536400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr7:50535800-50536400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr7:50535800-50539000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:50535800-50540800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:50535800-50546800	Weak transcription	Pancreas	Pancrea
44	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:50536000-50536200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr7:50536000-50536200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:50536000-50536200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr7:50536000-50536200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr7:50536000-50536200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr7:50536000-50536200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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