Variant report

Variant	rs1064608
Chromosome Location	chr11:47640429-47640430
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr11:47640234-47640518	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr11:47640251-47640439	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47638979..47640654-chr11:47662400..47665038,2	K562	blood:
2	chr11:47556504..47558457-chr11:47638712..47641328,2	K562	blood:

Variant related genes	Relation type
ENSG00000223187	TF binding region
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10838708	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10838738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039307	0.82[ASN][1000 genomes]
rs11039308	0.96[ASN][1000 genomes]
rs11039324	0.91[ASN][1000 genomes]
rs11039342	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039348	0.83[ASN][1000 genomes]
rs11039355	0.80[ASN][1000 genomes]
rs11602395	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11604680	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11604825	0.81[ASN][1000 genomes]
rs11605348	0.81[AMR][1000 genomes]
rs12363232	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419507	0.91[ASN][1000 genomes]
rs12419692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12421210	0.81[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787646	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12798028	0.83[ASN][1000 genomes]
rs12798346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12799623	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12803191	0.81[ASN][1000 genomes]
rs1317149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2030166	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2868459	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34910028	0.83[ASN][1000 genomes]
rs34923397	0.80[ASN][1000 genomes]
rs34958982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3781625	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3781626	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3781627	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56400411	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59360790	0.95[ASN][1000 genomes]
rs66749409	0.84[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7927771	1.00[CEU][hapmap]
rs7928842	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7945473	0.81[EUR][1000 genomes]
rs7947730	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs9909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3460885	chr11:47640287-47644381	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3500025	chr11:47640335-47647353	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3500026	chr11:47640335-47647353	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3460896	chr11:47640365-47644346	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3460907	chr11:47640365-47644346	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1064608	C1QTNF4	cis	Whole Blood	GTEx
rs1064608	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs1064608	SPI1	cis	multi-tissue	Pritchard
rs1064608	Hs.6637	cis	multi-tissue	Pritchard
rs1064608	C1QTNF4	cis	lung	GTEx
rs1064608	C1QTNF4	cis	Muscle Skeletal	GTEx
rs1064608	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs1064608	C1QTNF4	cis	multi-tissue	Pritchard
rs1064608	C1QTNF4	cis	Artery Tibial	GTEx
rs1064608	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs1064608	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs1064608	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47617600-47643200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:47621600-47647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:47621800-47642000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:47627800-47643200	Weak transcription	Pancreas	Pancrea
5	chr11:47628800-47642000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:47629800-47640800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:47629800-47642400	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:47630000-47641200	Weak transcription	Small Intestine	intestine
9	chr11:47630000-47642200	Weak transcription	Fetal Brain Male	brain
10	chr11:47630400-47648600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:47630400-47649600	Weak transcription	Fetal Heart	heart
12	chr11:47631200-47642400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:47631400-47640600	Weak transcription	Brain Germinal Matrix	brain
14	chr11:47633000-47640600	Weak transcription	Aorta	Aorta
15	chr11:47633000-47641800	Weak transcription	Spleen	Spleen
16	chr11:47633200-47641400	Weak transcription	Gastric	stomach
17	chr11:47633200-47642000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:47633200-47642000	Weak transcription	Esophagus	oesophagus
19	chr11:47633600-47641400	Weak transcription	Psoas Muscle	Psoas
20	chr11:47633600-47647200	Weak transcription	Right Ventricle	heart
21	chr11:47633800-47640600	Weak transcription	Lung	lung
22	chr11:47633800-47641800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:47635000-47642400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:47635400-47642000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:47635400-47643200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:47635800-47643200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:47636400-47642000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:47636600-47641800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:47636600-47661400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:47636800-47640600	Strong transcription	A549	lung
31	chr11:47636800-47653800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:47637000-47653400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:47637600-47648800	Strong transcription	Fetal Intestine Large	intestine
34	chr11:47637600-47650800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:47637600-47653200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:47637600-47653200	Strong transcription	Liver	Liver
37	chr11:47637600-47657200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr11:47637600-47660800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr11:47637600-47661200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:47637600-47663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr11:47637800-47641000	Strong transcription	Primary T cells from cord blood	blood
42	chr11:47637800-47642400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:47637800-47653200	Strong transcription	Left Ventricle	heart
44	chr11:47637800-47660400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:47637800-47661000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:47637800-47661000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr11:47638000-47641400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:47638000-47661400	Strong transcription	Fetal Thymus	thymus
49	chr11:47638000-47661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:47638200-47642200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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