Variant report

Variant	rs1317149
Chromosome Location	chr11:47486885-47486886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47486877..47488981-chr11:47490201..47491950,2	K562	blood:
2	chr11:47486712..47489555-chr11:47586746..47588709,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110536	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000213619	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1057233	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10742803	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs10769258	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs10769262	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs10838698	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs10838699	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs10838704	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10838706	0.83[ASN][1000 genomes]
rs10838708	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10838724	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838738	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs11039212	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap]
rs11039219	0.83[ASN][1000 genomes]
rs11039238	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11039255	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039265	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11570094	1.00[YRI][hapmap]
rs11600581	0.83[ASN][1000 genomes]
rs11601603	0.89[CEU][hapmap]
rs11604680	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11605672	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap]
rs12419692	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12798346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2053979	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2053980	0.81[ASN][1000 genomes]
rs2071304	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs2291119	1.00[YRI][hapmap]
rs2293577	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2293578	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2293580	0.85[ASN][1000 genomes]
rs2856650	1.00[YRI][hapmap]
rs2868459	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34958982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35184771	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35496532	0.84[ASN][1000 genomes]
rs35705029	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3781624	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3781625	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3781626	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3781627	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4752838	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4752990	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4752993	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]
rs4752994	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4752999	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs4992357	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap]
rs55927797	0.85[ASN][1000 genomes]
rs56400411	0.82[ASN][1000 genomes]
rs60075622	0.84[ASN][1000 genomes]
rs6485753	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs66749409	0.83[ASN][1000 genomes]
rs7106956	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7107726	0.83[ASN][1000 genomes]
rs7124681	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs755553	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs755554	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs755555	0.83[ASN][1000 genomes]
rs7925389	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7928842	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7937331	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7940536	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs896816	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap]

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	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1317149	C1QTNF4	cis	Muscle Skeletal	GTEx
rs1317149	SPI1	cis	multi-tissue	Pritchard
rs1317149	C1QTNF4	cis	Whole Blood	GTEx
rs1317149	C1QTNF4	cis	Artery Tibial	GTEx
rs1317149	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs1317149	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs1317149	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs1317149	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs1317149	C1QTNF4	cis	lung	GTEx
rs1317149	C1QTNF4	cis	multi-tissue	Pritchard
rs1317149	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs1317149	Hs.6637	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47457400-47488400	Weak transcription	Gastric	stomach
3	chr11:47471200-47488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:47471400-47489200	Weak transcription	HepG2	liver
5	chr11:47476000-47487400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:47476200-47488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:47476600-47487400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:47476600-47488400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:47476600-47488600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:47477000-47487600	Weak transcription	Brain Substantia Nigra	brain
11	chr11:47478200-47488400	Weak transcription	Esophagus	oesophagus
12	chr11:47479400-47488200	Weak transcription	Colonic Mucosa	Colon
13	chr11:47479400-47491200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:47479600-47489800	Weak transcription	Fetal Kidney	kidney
15	chr11:47479600-47491400	Weak transcription	Aorta	Aorta
16	chr11:47479800-47489000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:47479800-47494400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:47480000-47487800	Strong transcription	Fetal Stomach	stomach
19	chr11:47480000-47510000	Strong transcription	Thymus	Thymus
20	chr11:47480200-47488800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:47480600-47489000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:47480600-47508400	Strong transcription	Fetal Intestine Small	intestine
23	chr11:47480800-47487200	Strong transcription	Lung	lung
24	chr11:47480800-47511000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:47480800-47511400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:47481000-47498400	Strong transcription	NHEK	skin
27	chr11:47481200-47487400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:47481400-47488200	Weak transcription	Pancreas	Pancrea
29	chr11:47482200-47487000	Weak transcription	Fetal Brain Female	brain
30	chr11:47482200-47487400	Weak transcription	Brain Angular Gyrus	brain
31	chr11:47482200-47488800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:47482200-47489000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr11:47482400-47488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:47482600-47488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:47482600-47488600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:47482800-47488200	Weak transcription	Fetal Heart	heart
37	chr11:47483000-47487200	Weak transcription	NH-A	brain
38	chr11:47483200-47487200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:47483400-47487800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:47483400-47508800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:47483600-47487200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:47483600-47487600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:47483600-47511400	Strong transcription	Dnd41	blood
44	chr11:47483800-47488000	Weak transcription	Fetal Brain Male	brain
45	chr11:47484000-47488400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:47484200-47489000	Weak transcription	Psoas Muscle	Psoas
47	chr11:47484800-47487200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:47484800-47487600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:47484800-47488400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:47484800-47490800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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