Variant report

Variant	rs11563640
Chromosome Location	chr7:127000955-127000956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:126989599..126991125-chr7:126999110..127001691,2	K562	blood:
2	chr7:126999623..127001403-chr7:127005210..127006767,2	MCF-7	breast:
3	chr7:126999289..127001644-chr7:127001695..127003278,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF800-2	chr7:126999844-127004813	NONHSAT123138

Variant related genes	Relation type
ENSG00000224138	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10243318	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10250993	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11563330	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11563331	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11563457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11563465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532298	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12533653	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535410	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706782	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12706794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13222357	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13223068	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13234675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13239338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239894	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246076	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345206	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1361947	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1361948	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1557639	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17862361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862375	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17864191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17864199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17864200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17864202	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17864920	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17867841	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17869209	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1819774	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894725	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894726	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2106175	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55691590	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56317753	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957751	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs6978075	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs9632759	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017145	chr7:126995304-127015459	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11563640	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126987800-127020600	Weak transcription	Spleen	Spleen
2	chr7:126988200-127001000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:126988400-127001000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:126988400-127001000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:126988400-127001000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:126988400-127001000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:126988400-127001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:126988400-127001000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:126988400-127001000	Weak transcription	Aorta	Aorta
10	chr7:126988400-127001000	Weak transcription	Brain Angular Gyrus	brain
11	chr7:126988400-127001000	Weak transcription	Esophagus	oesophagus
12	chr7:126988400-127001000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:126988400-127001000	Weak transcription	Fetal Stomach	stomach
14	chr7:126988400-127001000	Weak transcription	Left Ventricle	heart
15	chr7:126988400-127001000	Weak transcription	Lung	lung
16	chr7:126988400-127001000	Weak transcription	Right Ventricle	heart
17	chr7:126988400-127001000	Weak transcription	Thymus	Thymus
18	chr7:126988400-127001000	Weak transcription	NH-A	brain
19	chr7:126988400-127001000	Weak transcription	NHLF	lung
20	chr7:126988400-127001200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:126988400-127002200	Weak transcription	Fetal Heart	heart
22	chr7:126988400-127004400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:126988400-127006400	Weak transcription	Psoas Muscle	Psoas
24	chr7:126988400-127012600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:126988400-127013000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:126988400-127013000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:126988400-127013200	Weak transcription	NHEK	skin
28	chr7:126988400-127013400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:126988400-127014000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:126988400-127030200	Weak transcription	Fetal Intestine Small	intestine
31	chr7:126988400-127031400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:126988400-127031400	Weak transcription	Colonic Mucosa	Colon
33	chr7:126988400-127031400	Weak transcription	Pancreas	Pancrea
34	chr7:126988600-127001000	Weak transcription	Fetal Lung	lung
35	chr7:126988600-127007000	Weak transcription	A549	lung
36	chr7:126988600-127013400	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:126988800-127005000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:126989000-127031000	Weak transcription	Fetal Brain Male	brain
39	chr7:126991600-127030400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr7:126993800-127001000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:126994000-127019800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr7:126994600-127002200	Strong transcription	K562	blood
43	chr7:126995200-127007800	Weak transcription	Brain Anterior Caudate	brain
44	chr7:126995400-127022600	Strong transcription	Dnd41	blood
45	chr7:126995600-127027600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:126996200-127013000	Weak transcription	Ovary	ovary
47	chr7:126996600-127001000	Weak transcription	Gastric	stomach
48	chr7:126996600-127001000	Weak transcription	HepG2	liver
49	chr7:126996600-127006400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr7:126996800-127010600	Strong transcription	Primary T cells fromperipheralblood	blood

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