Variant report

Variant	rs7947730
Chromosome Location	chr11:47786184-47786185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47785710..47787900-chr11:47788302..47790353,2	K562	blood:
2	chr11:47775684..47777811-chr11:47784921..47787606,4	K562	blood:
3	chr11:47775752..47779558-chr11:47781673..47786599,7	K562	blood:
4	chr11:47785352..47787641-chr11:47860317..47862615,2	K562	blood:
5	chr11:47785484..47788577-chr11:47791661..47794757,3	K562	blood:
6	chr11:47755457..47757278-chr11:47784612..47786909,2	K562	blood:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1064608	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10838738	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10838747	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039308	0.80[ASN][1000 genomes]
rs11039324	0.81[ASN][1000 genomes]
rs11039342	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039348	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039355	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039389	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039390	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039391	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039416	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039433	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11602339	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11602395	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604825	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11605774	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12361031	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364432	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12418852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12419692	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs12421210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12785833	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787330	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12787646	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12794570	0.95[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs12798109	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12803191	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17788930	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290850	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];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34128973	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34910028	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34923397	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35805829	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35902101	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35985502	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817334	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4752797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752856	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs4752857	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs4752873	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59360790	0.82[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7120333	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130758	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7927771	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7947730	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs7947730	MADD	cis	cerebellum	SCAN
rs7947730	SPI1	cis	lymphoblastoid	seeQTL
rs7947730	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs7947730	C1QTNF4	cis	Whole Blood	GTEx
rs7947730	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs7947730	C1QTNF4	cis	Muscle Skeletal	GTEx
rs7947730	C1QTNF4	cis	lung	GTEx
rs7947730	C1QTNF4	cis	lymphoblastoid	seeQTL
rs7947730	MTCH2	cis	cerebellum	SCAN
rs7947730	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7947730	SLC35C1	cis	parietal	SCAN
rs7947730	C1QTNF4	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47737000-47786200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:47737800-47786200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:47737800-47786200	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr11:47737800-47786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:47737800-47786400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:47737800-47786400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:47737800-47786400	Strong transcription	Fetal Thymus	thymus
8	chr11:47737800-47786800	Strong transcription	Placenta	Placenta
9	chr11:47738000-47786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:47738000-47786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:47738000-47786400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr11:47738000-47786800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:47738200-47786400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:47738400-47786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:47746400-47786200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr11:47747400-47786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:47747600-47786400	Strong transcription	Fetal Intestine Large	intestine
18	chr11:47747800-47786200	Strong transcription	A549	lung
19	chr11:47748600-47786200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:47748600-47786200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:47748800-47786200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:47753400-47786400	Strong transcription	Liver	Liver
23	chr11:47753600-47786400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:47759200-47786200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:47764800-47786200	Strong transcription	HSMM	muscle
26	chr11:47768000-47786600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:47769000-47787600	Weak transcription	Stomach Mucosa	stomach
28	chr11:47776000-47787400	Weak transcription	Psoas Muscle	Psoas
29	chr11:47777400-47786200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:47777400-47786200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:47777600-47786400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr11:47777600-47786800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:47778000-47786200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:47778000-47786200	Strong transcription	Adipose Nuclei	Adipose
35	chr11:47778000-47786400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:47778400-47786800	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:47778400-47787000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:47778600-47786200	Strong transcription	Primary T cells from cord blood	blood
39	chr11:47778600-47786200	Strong transcription	Fetal Brain Female	brain
40	chr11:47778600-47786400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:47778600-47786400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr11:47778600-47786600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:47778600-47786800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr11:47778800-47786600	Strong transcription	Left Ventricle	heart
45	chr11:47779000-47786200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:47779000-47786200	Strong transcription	Osteobl	bone
47	chr11:47779000-47786400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:47779000-47786800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:47779200-47786200	Strong transcription	Hela-S3	cervix
50	chr11:47779200-47786400	Strong transcription	Colonic Mucosa	Colon

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