Variant report

Variant	rs35705029
Chromosome Location	chr11:47459963-47459964
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47449067..47450905-chr11:47458013..47460570,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10742803	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769262	0.82[EUR][1000 genomes]
rs10838704	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838706	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838724	0.88[ASN][1000 genomes]
rs11039212	0.80[EUR][1000 genomes]
rs11039219	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039238	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039255	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11039265	0.84[ASN][1000 genomes]
rs11600581	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11601603	0.81[EUR][1000 genomes]
rs11604680	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11605672	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11607981	0.81[EUR][1000 genomes]
rs12802273	0.82[EUR][1000 genomes]
rs12803525	0.83[EUR][1000 genomes]
rs1317149	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1317164	0.86[EUR][1000 genomes]
rs2053979	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2053980	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293577	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293578	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293580	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2868459	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34958982	0.88[ASN][1000 genomes]
rs35184771	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35496532	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781624	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3781625	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781626	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3781627	0.88[ASN][1000 genomes]
rs4752832	0.81[ASN][1000 genomes]
rs4752838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752845	0.89[ASN][1000 genomes]
rs4752990	0.83[EUR][1000 genomes]
rs4752993	0.82[EUR][1000 genomes]
rs4752994	0.82[EUR][1000 genomes]
rs4752999	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55677087	0.81[EUR][1000 genomes]
rs55876153	0.83[EUR][1000 genomes]
rs55927797	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58965622	0.84[EUR][1000 genomes]
rs60075622	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485753	0.82[EUR][1000 genomes]
rs6485756	0.81[ASN][1000 genomes]
rs67472071	0.81[EUR][1000 genomes]
rs7106956	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107726	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7124681	0.90[ASN][1000 genomes]
rs755553	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs755554	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs755555	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7924485	0.83[EUR][1000 genomes]
rs7925389	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7937331	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35705029	C1QTNF4	cis	Muscle Skeletal	GTEx
rs35705029	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs35705029	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs35705029	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
3	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
4	chr11:47456400-47460200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:47456400-47460400	Weak transcription	HSMMtube	muscle
6	chr11:47456600-47463600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:47456600-47468600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:47457400-47488400	Weak transcription	Gastric	stomach
11	chr11:47457800-47469000	Weak transcription	Spleen	Spleen
12	chr11:47458800-47460000	Enhancers	Stomach Smooth Muscle	stomach
13	chr11:47458800-47460200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr11:47458800-47460600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr11:47459000-47460000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr11:47459000-47460000	Enhancers	Fetal Intestine Large	intestine
17	chr11:47459000-47460000	Enhancers	Lung	lung
18	chr11:47459000-47460000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:47459200-47460000	Enhancers	Adipose Nuclei	Adipose
20	chr11:47459200-47460000	Enhancers	Fetal Muscle Trunk	muscle
21	chr11:47459400-47462000	Weak transcription	HSMM	muscle
22	chr11:47459800-47460000	Active TSS	HepG2	liver
23	chr11:47459800-47460600	Enhancers	Liver	Liver
24	chr11:47459800-47462200	Weak transcription	Fetal Muscle Leg	muscle
25	chr11:47459800-47463000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:47459800-47464000	Weak transcription	Brain Anterior Caudate	brain
27	chr11:47459800-47464400	Weak transcription	Left Ventricle	heart
28	chr11:47459800-47466400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:47459800-47469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:47459800-47470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
32	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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