Variant report

Variant	rs7804472
Chromosome Location	chr7:128333758-128333759
allele	A/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	POLR2A	chr7:128333584-128333763	GM12878	blood:	n/a	n/a
2	MAX	chr7:128333325-128334086	K562	blood:	n/a	chr7:128333828-128333838
3	CBX3	chr7:128333727-128334129	K562	blood:	n/a	n/a
4	MAX	chr7:128333707-128333997	NB4	blood:	n/a	chr7:128333828-128333838
5	MAX	chr7:128333563-128334068	HepG2	liver:	n/a	chr7:128333828-128333838
6	MAX	chr7:128333545-128334020	HepG2	liver:	n/a	chr7:128333828-128333838
7	MAX	chr7:128333727-128334026	HepG2	liver:	n/a	chr7:128333828-128333838
8	E2F6	chr7:128333703-128333918	K562	blood:	n/a	n/a
9	USF1	chr7:128333706-128333999	K562	blood:	n/a	n/a
10	POLR2A	chr7:128333575-128333900	Hela-S3	cervix:	n/a	n/a
11	MAX	chr7:128333680-128333940	K562	blood:	n/a	chr7:128333828-128333838

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128331712..128335200-chr7:128335875..128338019,5	K562	blood:
2	chr7:128331833..128334672-chr7:128377724..128379634,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-6	chr7:128333504-128333978	NONHSAT123245

Variant related genes	Relation type
RNA5SP242	TF binding region
RNA5SP243	TF binding region
ENSG00000128595	Chromatin interaction
ENSG00000252866	Chromatin interaction
ENSG00000201041	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10085435	0.81[EUR][1000 genomes]
rs10224862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10233059	0.82[EUR][1000 genomes]
rs10241185	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10242806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10253131	0.84[EUR][1000 genomes]
rs10259359	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10270431	0.84[EUR][1000 genomes]
rs10270985	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10274878	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10276810	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10954205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11761312	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11766319	0.86[AMR][1000 genomes]
rs11768485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12333625	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12535238	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12536288	0.84[ASN][1000 genomes]
rs12706858	0.95[ASN][1000 genomes]
rs13224613	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13233377	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13235219	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13237593	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28521711	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs339070	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs339071	0.95[ASN][1000 genomes]
rs339074	0.95[ASN][1000 genomes]
rs339079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34120723	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34490491	0.84[EUR][1000 genomes]
rs34751214	0.84[EUR][1000 genomes]
rs35247963	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35336068	0.90[AFR][1000 genomes]
rs35825132	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35871589	0.85[EUR][1000 genomes]
rs3816421	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4289745	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6467181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs6467201	0.84[EUR][1000 genomes]
rs6467205	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6943737	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6946179	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6954329	0.93[AFR][1000 genomes]
rs6960296	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6961754	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6967393	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6971819	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6972787	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6977126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71548762	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7776915	0.81[EUR][1000 genomes]
rs7778731	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7787764	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7790478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7794447	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7810047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9690934	0.84[EUR][1000 genomes]
rs9692416	0.84[EUR][1000 genomes]
rs9768808	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9769753	0.84[EUR][1000 genomes]

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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv966738	chr7:128325654-128339129	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7804472	CICP14	cis	Thyroid	GTEx
rs7804472	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs7804472	RP11-274B21.10	cis	Skin Sun Exposed Lower leg	GTEx
rs7804472	CICP14	cis	Esophagus Muscularis	GTEx
rs7804472	RP11-274B21.10	cis	Nerve Tibial	GTEx
rs7804472	CICP14	cis	lung	GTEx
rs7804472	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs7804472	RP11-274B21.10	cis	Esophagus Mucosa	GTEx
rs7804472	RP11-274B21.10	cis	Thyroid	GTEx
rs7804472	KLF14	cis	parietal	SCAN
rs7804472	CICP14	cis	Nerve Tibial	GTEx
rs7804472	CICP14	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128302400-128337200	Weak transcription	Gastric	stomach
2	chr7:128313600-128337200	Weak transcription	Right Atrium	heart
3	chr7:128320200-128337200	Weak transcription	NHLF	lung
4	chr7:128323400-128337200	Weak transcription	Left Ventricle	heart
5	chr7:128324200-128337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:128324400-128337200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:128325600-128333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:128325600-128337000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:128326000-128337200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:128328000-128334000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:128328000-128334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:128328000-128337000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:128328000-128337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:128328000-128337200	Weak transcription	HSMMtube	muscle
15	chr7:128328000-128337200	Weak transcription	NH-A	brain
16	chr7:128328200-128337000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:128328800-128337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:128329000-128337200	Weak transcription	HSMM	muscle
19	chr7:128329400-128337200	Weak transcription	Pancreas	Pancrea
20	chr7:128332800-128334400	Enhancers	K562	blood
21	chr7:128333200-128335200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:128333400-128334000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:128333600-128334000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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