Variant report

Variant	rs60075622
Chromosome Location	chr11:47449101-47449102
allele	G/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	HCFC1	chr11:47445853-47449989	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:47447548-47449438	HepG2	liver:	n/a	n/a
3	HA-E2F1	chr11:47447629-47449101	MCF-7	breast:	n/a	chr11:47448076-47448087 chr11:47448119-47448128 chr11:47448028-47448037 chr11:47448051-47448062 chr11:47448051-47448063
4	POLR2A	chr11:47448530-47449341	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47448979..47451743-chr11:47463608..47465807,2	K562	blood:
2	chr11:47198368..47200069-chr11:47446814..47449315,2	MCF-7	breast:
3	chr11:47446295..47450524-chr11:47461441..47464685,6	MCF-7	breast:
4	chr11:47449067..47450905-chr11:47458013..47460570,2	MCF-7	breast:
5	chr11:47196939..47199221-chr11:47446629..47449473,2	K562	blood:
6	chr11:47398927..47401374-chr11:47448250..47449858,2	K562	blood:

Variant related genes	Relation type
PSMC3	TF binding region
ENSG00000165917	Chromatin interaction
ENSG00000252327	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000066336	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1057233	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10734557	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10742803	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769258	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10769262	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838698	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10838699	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10838704	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838706	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838708	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10838724	0.82[ASN][1000 genomes]
rs11039199	0.83[EUR][1000 genomes]
rs11039200	0.83[EUR][1000 genomes]
rs11039202	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11039203	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11039212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039219	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039238	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039255	0.85[ASN][1000 genomes]
rs11039265	0.81[ASN][1000 genomes]
rs11600581	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601603	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11604680	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605672	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11607981	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12146565	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12802273	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12803525	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1317149	0.84[ASN][1000 genomes]
rs1317164	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1542321	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2053979	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053980	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084946	0.87[EUR][1000 genomes]
rs2293577	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293578	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293580	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2856661	0.80[AMR][1000 genomes]
rs2868459	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34958982	0.81[ASN][1000 genomes]
rs35184771	0.86[ASN][1000 genomes]
rs35496532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35705029	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35996350	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3740686	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3781624	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781626	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781627	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752827	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4752832	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752838	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752845	0.82[ASN][1000 genomes]
rs4752987	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4752990	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4752993	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752994	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4752999	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4992357	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55677087	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55876153	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55927797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56030824	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58965622	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485753	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6485756	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67116452	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67472071	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7105851	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7106956	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7107726	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111957	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7124681	0.84[ASN][1000 genomes]
rs755553	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755554	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755555	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924485	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7925299	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7925389	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7928163	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7928419	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7937331	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7940536	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs896815	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896816	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs935914	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	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
5	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs60075622	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs60075622	C1QTNF4	cis	Muscle Skeletal	GTEx
rs60075622	SPI1	cis	multi-tissue	Pritchard
rs60075622	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs60075622	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47447000-47449200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr11:47447200-47449200	Bivalent/Poised TSS	HepG2	liver
3	chr11:47447200-47449200	Active TSS	NHEK	skin
4	chr11:47447400-47449200	Active TSS	HMEC	breast
5	chr11:47447600-47449200	Active TSS	Liver	Liver
6	chr11:47447600-47449200	Active TSS	Monocytes-CD14+_RO01746	blood
7	chr11:47448600-47449600	Weak transcription	HSMMtube	muscle
8	chr11:47448600-47452000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:47448600-47452200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:47448600-47459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:47448800-47449800	Flanking Active TSS	Hela-S3	cervix
13	chr11:47448800-47452000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:47448800-47452000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:47448800-47453000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:47448800-47453000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:47448800-47454800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:47449000-47449200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr11:47449000-47449200	Enhancers	Primary B cells from peripheral blood	blood
20	chr11:47449000-47449200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr11:47449000-47449200	Enhancers	Fetal Muscle Leg	muscle
22	chr11:47449000-47449400	Flanking Active TSS	A549	lung
23	chr11:47449000-47451400	Weak transcription	Fetal Thymus	thymus
24	chr11:47449000-47451600	Weak transcription	Thymus	Thymus
25	chr11:47449000-47452000	Weak transcription	Primary T cells from cord blood	blood
26	chr11:47449000-47452200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:47449000-47453200	Weak transcription	Psoas Muscle	Psoas
28	chr11:47449000-47454800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:47449000-47454800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:47449000-47454800	Weak transcription	HSMM	muscle
31	chr11:47449000-47457200	Weak transcription	Right Atrium	heart
32	chr11:47449000-47459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:47449000-47459400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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