Variant report

Variant	rs2348667
Chromosome Location	chr7:48074957-48074958
allele	C/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	CREB1	chr7:48074867-48075282	A549	lung:	n/a	n/a
2	CTCF	chr7:48074900-48075050	NHLF	lung:	n/a	n/a
3	CTCF	chr7:48074884-48075063	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr7:48074860-48075010	HA-sp	spinal cord:	n/a	n/a
5	RCOR1	chr7:48074312-48075590	IMR90	lung:	n/a	n/a
6	MYC	chr7:48074781-48075133	MCF-7	breast:	n/a	chr7:48075091-48075100
7	CHD2	chr7:48074855-48075359	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr7:48074884-48075055	A549	lung:	n/a	n/a
9	MAX	chr7:48074726-48076108	H1-hESC	embryonic stem cell:	n/a	chr7:48075091-48075100
10	CTCF	chr7:48074799-48075131	MCF-7	breast:	n/a	chr7:48075066-48075079
11	CTCF	chr7:48074883-48075048	H1-hESC	embryonic stem cell:	n/a	n/a
12	RFX5	chr7:48074438-48075537	SK-N-SH	brain:	n/a	chr7:48075090-48075105 chr7:48075009-48075018 chr7:48075090-48075105 chr7:48075090-48075105
13	MAX	chr7:48074797-48075196	A549	lung:	n/a	chr7:48075091-48075100
14	CTCF	chr7:48074848-48075110	GM19238	blood:	n/a	chr7:48075066-48075079
15	CTCF	chr7:48074875-48075078	GM19240	blood:	n/a	n/a
16	MXI1	chr7:48074899-48075587	HepG2	liver:	n/a	chr7:48075089-48075104 chr7:48075091-48075106
17	CTCF	chr7:48074860-48075010	HVMF	connective:	n/a	n/a
18	GTF2F1	chr7:48074957-48075140	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr7:48074820-48074970	GM12872	blood:	n/a	n/a
20	CTCF	chr7:48074820-48074970	HRPEpiC	eye:	n/a	n/a
21	RAD21	chr7:48074872-48075258	A549	lung:	n/a	n/a
22	FOS	chr7:48074955-48075163	MCF10A-Er-Src	breast:	n/a	chr7:48075008-48075017
23	CTCF	chr7:48074940-48075090	SAEC	small airway:	n/a	chr7:48075066-48075079
24	PAX5	chr7:48074853-48075256	GM12892	blood:	n/a	chr7:48074986-48074995
25	CTCF	chr7:48074940-48075090	HA-sp	spinal cord:	n/a	chr7:48075066-48075079
26	NFYB	chr7:48074843-48075182	K562	blood:	n/a	chr7:48075006-48075021 chr7:48075038-48075053 chr7:48075038-48075053 chr7:48075006-48075021 chr7:48075007-48075021
27	CTCF	chr7:48074920-48075070	GM06990	blood:	n/a	n/a
28	CTCF	chr7:48074920-48075070	HRPEpiC	eye:	n/a	n/a
29	CTCF	chr7:48074880-48075030	HepG2	liver:	n/a	n/a
30	CTCF	chr7:48074940-48075090	HPAF	blood vessel:	n/a	chr7:48075066-48075079
31	CTCF	chr7:48074880-48075030	GM12870	blood:	n/a	n/a
32	CTCF	chr7:48074900-48075050	AG04449	skin:	n/a	n/a
33	SIN3AK20	chr7:48074830-48075612	PANC-1	pancreas:	n/a	n/a
34	MXI1	chr7:48074710-48076005	H1-hESC	embryonic stem cell:	n/a	chr7:48075089-48075104 chr7:48075091-48075106
35	CTCF	chr7:48074920-48075070	GM12866	blood:	n/a	n/a
36	MAX	chr7:48074759-48076153	ECC-1	luminal epithelium:	n/a	chr7:48075091-48075100
37	NFIC	chr7:48074754-48075353	ECC-1	luminal epithelium:	n/a	n/a
38	SIN3AK20	chr7:48074859-48075378	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr7:48074920-48075070	Caco-2	colon:	n/a	n/a
40	FOS	chr7:48074864-48075207	GM12878	blood:	n/a	chr7:48075008-48075017
41	CTCF	chr7:48074940-48075090	Caco-2	colon:	n/a	chr7:48075066-48075079
42	CTCF	chr7:48074904-48075135	Fibrobl	skin:	n/a	chr7:48075066-48075079
43	CTCF	chr7:48074920-48075070	AG09309	skin:	n/a	n/a
44	FOXM1	chr7:48074898-48075362	GM12878	blood:	n/a	n/a
45	HA-E2F1	chr7:48074811-48076158	MCF-7	breast:	n/a	chr7:48075880-48075887 chr7:48075880-48075887 chr7:48075021-48075030 chr7:48074983-48074993 chr7:48075010-48075019 chr7:48075880-48075887 chr7:48075064-48075073
46	CTCF	chr7:48074900-48075050	GM12866	blood:	n/a	n/a
47	CTCF	chr7:48074875-48075183	Spleen_OC	spleen:	n/a	chr7:48075066-48075079
48	MXI1	chr7:48074509-48076029	IMR90	lung:	n/a	chr7:48075089-48075104 chr7:48075091-48075106
49	MAX	chr7:48074742-48075312	HepG2	liver:	n/a	chr7:48075091-48075100
50	ZNF143	chr7:48074957-48075227	H1-hESC	embryonic stem cell:	n/a	chr7:48074983-48074993 chr7:48075063-48075073

Variant related genes	Relation type
C7orf57	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10225968	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10247913	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10253220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10253238	0.83[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10256256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10261930	0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs10951937	0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10951938	0.85[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10951940	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10951941	0.91[CEU][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10951942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11761275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11762077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11764799	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11766144	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11766891	0.95[EUR][1000 genomes]
rs11767002	0.95[CEU][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11768277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11772387	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11772633	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11773348	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12535580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12702405	0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12702406	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1318327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13230023	0.82[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs1574242	0.95[CEU][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1915960	0.95[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs1915962	0.91[CEU][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1915965	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1915966	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1915967	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915968	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140113	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2348666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2348669	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2348670	0.85[EUR][1000 genomes]
rs2881991	0.90[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs2881992	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4332046	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4618593	0.87[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs6978838	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6979699	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7357251	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357327	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7456745	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7779252	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7791084	0.86[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7791572	0.86[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7791823	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807611	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7807612	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7807654	0.86[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7807750	0.86[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7808462	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9690905	0.91[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2348667	UPP1	cis	Muscle Skeletal	GTEx
rs2348667	C7orf57	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48074200-48075400	Active TSS	Brain Angular Gyrus	brain
2	chr7:48074600-48075000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr7:48074600-48075000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr7:48074600-48075000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:48074600-48075000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:48074600-48075000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:48074600-48075000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr7:48074600-48075000	Enhancers	Stomach Smooth Muscle	stomach
9	chr7:48074600-48075000	Bivalent/Poised TSS	A549	lung
10	chr7:48074600-48075000	Active TSS	GM12878-XiMat	blood
11	chr7:48074600-48075000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
12	chr7:48074600-48075200	Active TSS	Brain Germinal Matrix	brain
13	chr7:48074600-48075200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr7:48074600-48075200	Active TSS	HMEC	breast
15	chr7:48074600-48075200	Active TSS	Osteobl	bone
16	chr7:48074600-48075400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:48074600-48075400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:48074600-48075400	Active TSS	Brain Anterior Caudate	brain
19	chr7:48074600-48075400	Active TSS	Brain Cingulate Gyrus	brain
20	chr7:48074600-48075400	Active TSS	Brain Hippocampus Middle	brain
21	chr7:48074600-48075400	Active TSS	Brain Substantia Nigra	brain
22	chr7:48074600-48075400	Bivalent Enhancer	Fetal Brain Male	brain
23	chr7:48074600-48075400	Bivalent/Poised TSS	Fetal Brain Female	brain
24	chr7:48074600-48076000	Bivalent/Poised TSS	HSMMtube	muscle
25	chr7:48074800-48075000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:48074800-48075000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:48074800-48075000	Bivalent Enhancer	Primary B cells from cord blood	blood
28	chr7:48074800-48075000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:48074800-48075000	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr7:48074800-48075000	Active TSS	Colonic Mucosa	Colon
31	chr7:48074800-48075000	Enhancers	Esophagus	oesophagus
32	chr7:48074800-48075000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr7:48074800-48075000	Bivalent Enhancer	Fetal Thymus	thymus
34	chr7:48074800-48075000	Enhancers	Gastric	stomach
35	chr7:48074800-48075000	Active TSS	Right Ventricle	heart
36	chr7:48074800-48075200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:48074800-48075200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:48074800-48075200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:48074800-48075200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:48074800-48075200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:48074800-48075200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:48074800-48075200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:48074800-48075200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:48074800-48075200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:48074800-48075200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
46	chr7:48074800-48075200	Active TSS	Rectal Smooth Muscle	rectum
47	chr7:48074800-48075200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
48	chr7:48074800-48075200	Bivalent/Poised TSS	Thymus	Thymus
49	chr7:48074800-48075400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr7:48074800-48075400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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