Variant report

Variant	rs34958982
Chromosome Location	chr11:47547046-47547047
allele	C/T
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	MAFF	chr11:47546897-47547073	HepG2	liver:	n/a	chr11:47546915-47546933
2	MAFK	chr11:47546772-47547077	HepG2	liver:	n/a	chr11:47546917-47546933 chr11:47546917-47546928 chr11:47546917-47546928 chr11:47546917-47546932

No.	Distal block	Cell Line	Cell type
1	chr11:47546764..47549140-chr11:47573105..47575374,2	MCF-7	breast:
2	chr11:47546750..47549859-chr11:47604197..47608335,3	K562	blood:
3	chr11:47545148..47547980-chr11:47586701..47589133,2	MCF-7	breast:

Variant related genes	Relation type
CELF1	TF binding region
ENSG00000110536	Chromatin interaction
ENSG00000196666	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1057233	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10742803	0.87[CEU][hapmap];0.82[ASN][1000 genomes]
rs10769258	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap]
rs10769262	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs10838698	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap]
rs10838699	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs10838704	0.80[ASN][1000 genomes]
rs10838706	0.80[ASN][1000 genomes]
rs10838708	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10838724	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838738	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10838747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11039212	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs11039219	0.80[ASN][1000 genomes]
rs11039238	0.87[ASN][1000 genomes]
rs11039255	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039265	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11570094	1.00[YRI][hapmap]
rs11600581	0.80[ASN][1000 genomes]
rs11601603	0.89[CEU][hapmap]
rs11604680	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11605672	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs12419692	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs12787112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12798028	0.81[ASN][1000 genomes]
rs12798346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1317149	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]
rs2030166	0.81[ASN][1000 genomes]
rs2053979	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2071304	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs2293577	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293578	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs2293580	0.82[ASN][1000 genomes]
rs2856650	1.00[YRI][hapmap]
rs2868459	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs35184771	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35496532	0.83[ASN][1000 genomes]
rs35705029	0.88[ASN][1000 genomes]
rs3740689	0.94[LWK][hapmap]
rs3781624	0.81[ASN][1000 genomes]
rs3781625	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3781626	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3781627	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752838	0.88[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752990	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs4752993	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs4752994	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs4752999	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs4992357	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap]
rs55927797	0.82[ASN][1000 genomes]
rs56400411	0.83[ASN][1000 genomes]
rs60075622	0.81[ASN][1000 genomes]
rs6485753	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs66749409	0.85[ASN][1000 genomes]
rs7106956	0.88[ASN][1000 genomes]
rs7107726	0.80[ASN][1000 genomes]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs755553	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[ASN][1000 genomes]
rs755554	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs755555	0.80[ASN][1000 genomes]
rs7925389	0.88[ASN][1000 genomes]
rs7928842	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7937331	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7940536	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs896816	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][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	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
2	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
3	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs34958982	C1QTNF4	cis	Whole Blood	GTEx
rs34958982	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs34958982	MTCH2	cis	cerebellum	SCAN
rs34958982	SLC35C1	cis	parietal	SCAN
rs34958982	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs34958982	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs34958982	SPI1	cis	lymphoblastoid	seeQTL
rs34958982	ACP2	cis	lymphoblastoid	seeQTL
rs34958982	MADD	cis	cerebellum	SCAN
rs34958982	C1QTNF4	cis	Artery Tibial	GTEx
rs34958982	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs34958982	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs34958982	C1QTNF4	cis	Muscle Skeletal	GTEx
rs34958982	C1QTNF4	cis	lymphoblastoid	seeQTL
rs34958982	C1QTNF4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47524800-47549600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:47540600-47549000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr11:47542400-47549000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:47543200-47547800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:47543400-47549000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr11:47543600-47548400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:47544200-47547800	Enhancers	Adipose Nuclei	Adipose
8	chr11:47544200-47548000	Enhancers	Primary B cells from peripheral blood	blood
9	chr11:47544200-47548200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:47544400-47547200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr11:47544400-47547200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:47544400-47547400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:47544400-47547400	Enhancers	Small Intestine	intestine
14	chr11:47544400-47547800	Enhancers	Fetal Thymus	thymus
15	chr11:47544400-47549400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr11:47544600-47547200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr11:47544800-47547200	Enhancers	Brain Hippocampus Middle	brain
18	chr11:47544800-47547400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr11:47544800-47547600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:47544800-47547800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:47544800-47547800	Enhancers	Brain Substantia Nigra	brain
22	chr11:47544800-47548000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr11:47544800-47548000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr11:47544800-47550000	Enhancers	HepG2	liver
25	chr11:47544800-47550400	Enhancers	Liver	Liver
26	chr11:47545000-47547200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:47545000-47547200	Enhancers	Ovary	ovary
28	chr11:47545000-47547400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr11:47545000-47547800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:47545000-47547800	Enhancers	Right Ventricle	heart
31	chr11:47545000-47547800	Enhancers	Spleen	Spleen
32	chr11:47545000-47548000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr11:47545000-47548000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr11:47545000-47548200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr11:47545400-47547200	Enhancers	Primary B cells from cord blood	blood
36	chr11:47545400-47547800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:47545400-47547800	Enhancers	Brain Cingulate Gyrus	brain
38	chr11:47545600-47547200	Enhancers	HUVEC	blood vessel
39	chr11:47545600-47547400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr11:47545600-47547400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:47545800-47547400	Enhancers	NHDF-Ad	bronchial
42	chr11:47545800-47547600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:47546000-47547400	Enhancers	K562	blood
44	chr11:47546000-47547600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:47546000-47547800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:47546000-47547800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr11:47546000-47548000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr11:47546000-47572400	Weak transcription	Fetal Intestine Large	intestine
49	chr11:47546200-47547200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr11:47546200-47547200	Enhancers	Fetal Muscle Leg	muscle

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