Variant report

Variant	rs11993959
Chromosome Location	chr8:55058591-55058592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:55057740..55060446-chr8:55064818..55067439,2	K562	blood:
2	chr8:54933508..54935660-chr8:55057965..55060583,2	K562	blood:
3	chr8:55053583..55055531-chr8:55058324..55060040,2	K562	blood:
4	chr8:55046961..55051250-chr8:55057827..55066628,8	K562	blood:
5	chr8:55010890..55013599-chr8:55056433..55059069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137547	Chromatin interaction
ENSG00000187735	Chromatin interaction
ENSG00000251835	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10216491	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1039926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10504161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.99[ASN][1000 genomes]
rs1050523	0.87[CHB][hapmap];0.84[GIH][hapmap]
rs10958396	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10958397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11984645	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11984672	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11986577	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs11991952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11994629	0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs11996128	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114043	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114739	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679103	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12679542	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12681024	0.81[EUR][1000 genomes]
rs13261058	0.84[EUR][1000 genomes]
rs13276927	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13277185	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16919782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008122	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271567	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292589	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2375696	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28573859	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34168614	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34997387	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4440612	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs4506187	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4737479	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs4737487	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4737488	0.85[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4737503	0.90[MEX][hapmap]
rs4738519	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4738678	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60183530	0.91[EUR][1000 genomes]
rs61213253	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61271559	0.91[EUR][1000 genomes]
rs61477279	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6473909	0.91[EUR][1000 genomes]
rs6473911	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6473913	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6473914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.99[ASN][1000 genomes]
rs6473915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983694	0.91[EUR][1000 genomes]
rs7011379	0.89[EUR][1000 genomes]
rs7011430	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7012031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71517558	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72614666	0.91[EUR][1000 genomes]
rs72614670	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72614671	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7463083	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs7464767	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs7830051	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7842911	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9298497	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs952194	0.87[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs981638	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1026869	chr8:54989732-55089360	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11993959	MRPL15	cis	cerebellum	SCAN
rs11993959	MRPL15	Cis_1M	lymphoblastoid	RTeQTL
rs11993959	LYPLA1	cis	lymphoblastoid	seeQTL
rs11993959	TCEA1	cis	lymphoblastoid	seeQTL
rs11993959	MRPL15	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:55048600-55065600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:55048600-55066200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:55048800-55063200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:55049000-55061800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr8:55049000-55062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr8:55049000-55065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr8:55049200-55061600	Strong transcription	Osteobl	bone
8	chr8:55049200-55063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:55049200-55063800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr8:55049200-55064000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:55049200-55064000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:55049200-55064000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:55049200-55064000	Strong transcription	Fetal Intestine Large	intestine
14	chr8:55049200-55064200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr8:55049200-55064600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:55049400-55061600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr8:55049400-55063600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:55049400-55063800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:55049400-55064000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:55049400-55064000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:55049400-55064000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr8:55049400-55064600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr8:55049600-55062000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:55049600-55064000	Strong transcription	Adipose Nuclei	Adipose
25	chr8:55049800-55063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr8:55049800-55064000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr8:55050000-55063000	Strong transcription	HMEC	breast
28	chr8:55050000-55063800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr8:55050600-55063800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr8:55052000-55061600	Strong transcription	NH-A	brain
31	chr8:55052000-55061800	Strong transcription	K562	blood
32	chr8:55052200-55061400	Strong transcription	Hela-S3	cervix
33	chr8:55052200-55061800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:55052200-55063200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:55052400-55061600	Strong transcription	NHEK	skin
36	chr8:55052600-55062200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:55052600-55063200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:55052600-55065600	Weak transcription	Fetal Heart	heart
39	chr8:55053600-55060800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:55053600-55061400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:55053600-55061400	Strong transcription	NHLF	lung
42	chr8:55053600-55061800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr8:55053600-55061800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:55053600-55061800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr8:55053600-55063000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr8:55053600-55063800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr8:55053600-55064000	Strong transcription	Fetal Thymus	thymus
48	chr8:55053800-55062800	Strong transcription	Placenta	Placenta
49	chr8:55054600-55062800	Strong transcription	Fetal Stomach	stomach
50	chr8:55054600-55063200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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