Variant report

Variant	rs1868588
Chromosome Location	chr7:112580395-112580396
allele	A/C
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	chr7:112579467-112580808	U87	brain:	n/a	n/a
2	POLR2A	chr7:112580027-112580619	GM12892	blood:	n/a	n/a
3	ELF1	chr7:112579664-112580625	MCF-7	breast:	n/a	chr7:112580030-112580039
4	TAF1	chr7:112579500-112580601	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr7:112580007-112580566	HepG2	liver:	n/a	n/a
6	SP1	chr7:112579753-112580399	GM12878	blood:	n/a	chr7:112580068-112580082 chr7:112579873-112579887 chr7:112580071-112580082 chr7:112580010-112580031 chr7:112580071-112580083
7	POLR2A	chr7:112579526-112581015	GM12878	blood:	n/a	n/a
8	USF2	chr7:112580229-112580459	HepG2	liver:	n/a	n/a
9	TAF1	chr7:112580216-112580480	GM12892	blood:	n/a	n/a
10	POLR2A	chr7:112579600-112580912	GM19099	blood:	n/a	n/a
11	YY1	chr7:112579695-112580677	GM12878	blood:	n/a	chr7:112580021-112580035
12	TBL1XR1	chr7:112579682-112580739	K562	blood:	n/a	n/a
13	POLR2A	chr7:112579499-112580672	K562	blood:	n/a	n/a
14	MXI1	chr7:112578922-112580907	GM12878	blood:	n/a	n/a
15	ELK1	chr7:112579828-112580629	GM12878	blood:	n/a	n/a
16	MAFF	chr7:112580092-112580484	HepG2	liver:	n/a	n/a
17	POLR2A	chr7:112579584-112580760	HepG2	liver:	n/a	n/a
18	POLR2A	chr7:112579625-112580823	PBDE	blood:	n/a	n/a
19	ELF1	chr7:112579521-112580401	GM12878	blood:	n/a	chr7:112580030-112580039
20	TBP	chr7:112579274-112580745	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr7:112579755-112580590	A549	lung:	n/a	n/a
22	USF1	chr7:112579919-112580502	SK-N-SH_RA	brain:	n/a	n/a
23	RCOR1	chr7:112579842-112580585	GM12878	blood:	n/a	n/a
24	SRF	chr7:112580236-112580527	K562	blood:	n/a	n/a
25	CUX1	chr7:112579922-112580538	GM12878	blood:	n/a	n/a
26	TAF1	chr7:112579648-112580613	K562	blood:	n/a	n/a
27	POLR2A	chr7:112579612-112580660	GM12878	blood:	n/a	n/a
28	HDAC2	chr7:112579466-112580562	MCF-7	breast:	n/a	n/a
29	RCOR1	chr7:112579811-112580407	HepG2	liver:	n/a	n/a
30	POLR2A	chr7:112579888-112580609	K562	blood:	n/a	n/a
31	POLR2A	chr7:112580020-112580805	K562	blood:	n/a	n/a
32	SP1	chr7:112579650-112580415	A549	lung:	n/a	chr7:112580068-112580082 chr7:112579873-112579887 chr7:112580071-112580082 chr7:112580010-112580031 chr7:112580071-112580083
33	SIN3AK20	chr7:112579361-112580549	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr7:112579441-112580573	GM19193	blood:	n/a	n/a
35	POLR2A	chr7:112580075-112580547	GM12891	blood:	n/a	n/a
36	POLR2A	chr7:112579349-112580919	GM18505	blood:	n/a	n/a
37	ATF2	chr7:112580038-112580496	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr7:112580041-112580608	A549	lung:	n/a	n/a
39	NFYB	chr7:112579732-112580710	GM12878	blood:	n/a	chr7:112579966-112579976 chr7:112580006-112580021
40	MAZ	chr7:112579008-112580815	K562	blood:	n/a	n/a
41	MYC	chr7:112579551-112580852	NB4	blood:	n/a	n/a
42	ELF1	chr7:112579559-112580568	K562	blood:	n/a	chr7:112580030-112580039
43	HDAC2	chr7:112580112-112580992	K562	blood:	n/a	n/a
44	POLR2A	chr7:112580040-112580597	GM12892	blood:	n/a	n/a
45	POLR2A	chr7:112579667-112580759	PFSK-1	brain:	n/a	n/a
46	JUN	chr7:112579843-112580662	K562	blood:	n/a	n/a
47	POLR2A	chr7:112579488-112580751	SK-N-MC	brain:	n/a	n/a
48	TBP	chr7:112579884-112580582	HepG2	liver:	n/a	n/a
49	POLR2A	chr7:112579150-112580782	K562	blood:	n/a	n/a
50	NRF1	chr7:112578593-112580941	SK-N-SH	brain:	n/a	chr7:112580161-112580175 chr7:112580161-112580172 chr7:112579458-112579467 chr7:112580160-112580171 chr7:112580206-112580217 chr7:112580161-112580170 chr7:112580158-112580172 chr7:112580208-112580217

No.	Distal block	Cell Line	Cell type
1	chr6:129642024..129642655-chr7:112579975..112580488,2	MCF-7	breast:
2	chr7:112580392..112582093-chr7:112599898..112601408,2	MCF-7	breast:
3	chr7:112428924..112430644-chr7:112579193..112581843,2	K562	blood:

Variant related genes	Relation type
C7orf60	TF binding region
ENSG00000146802	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10227777	1.00[EUR][1000 genomes]
rs10228144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229725	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10232962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10265199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277252	1.00[EUR][1000 genomes]
rs10500013	1.00[CHB][hapmap]
rs12112310	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12112671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17159980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17160084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060636	1.00[CHB][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28435304	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546198	1.00[ASN][1000 genomes]
rs28560010	1.00[ASN][1000 genomes]
rs28584529	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601694	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28603026	1.00[ASN][1000 genomes]
rs28624855	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28722087	1.00[ASN][1000 genomes]
rs6964755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965803	1.00[EUR][1000 genomes]
rs6968530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs6968845	1.00[ASN][1000 genomes]
rs6973297	1.00[ASN][1000 genomes]
rs73196918	1.00[ASN][1000 genomes]
rs7341402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73718117	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73718119	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73718127	1.00[ASN][1000 genomes]
rs73718130	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73718137	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777041	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7778342	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7798366	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7800661	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7806160	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2754368	chr7:112483049-112588049	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3692941	chr7:112571420-112614215	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv1795316	chr7:112577657-112588734	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv1027981	chr7:112577657-112613212	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112576800-112580800	Active TSS	Left Ventricle	heart
2	chr7:112577400-112580800	Active TSS	Right Ventricle	heart
3	chr7:112577600-112580600	Active TSS	Brain Angular Gyrus	brain
4	chr7:112577600-112580800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:112577600-112581000	Active TSS	Fetal Brain Female	brain
6	chr7:112577600-112581400	Active TSS	Aorta	Aorta
7	chr7:112577800-112580600	Active TSS	HSMMtube	muscle
8	chr7:112578000-112580600	Active TSS	Brain Anterior Caudate	brain
9	chr7:112578000-112580600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr7:112578000-112580800	Active TSS	NHLF	lung
11	chr7:112578000-112581000	Active TSS	Brain Germinal Matrix	brain
12	chr7:112578200-112580400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:112578200-112580600	Active TSS	Fetal Heart	heart
14	chr7:112578200-112580800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:112578200-112581000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr7:112578400-112580400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:112578400-112580400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:112578400-112580400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:112578400-112580400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:112578400-112580400	Active TSS	Fetal Stomach	stomach
21	chr7:112578400-112580400	Active TSS	GM12878-XiMat	blood
22	chr7:112578400-112580600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:112578400-112580600	Active TSS	Fetal Intestine Large	intestine
24	chr7:112578400-112580600	Active TSS	Fetal Intestine Small	intestine
25	chr7:112578400-112580800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:112578400-112581000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:112578600-112580400	Active TSS	Muscle Satellite Cultured Cells	--
28	chr7:112578600-112580400	Active TSS	Fetal Kidney	kidney
29	chr7:112578600-112580600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:112578600-112580600	Active TSS	Fetal Brain Male	brain
31	chr7:112578600-112580800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr7:112578600-112580800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:112578600-112580800	Active TSS	Ovary	ovary
34	chr7:112578600-112581000	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr7:112578600-112581000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:112578600-112581000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:112578600-112581000	Active TSS	Colonic Mucosa	Colon
38	chr7:112578600-112581000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr7:112578600-112581000	Active TSS	A549	lung
40	chr7:112578600-112581200	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr7:112578800-112580400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:112578800-112580400	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr7:112578800-112580400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr7:112578800-112580400	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr7:112578800-112580400	Active TSS	Fetal Lung	lung
46	chr7:112578800-112580400	Active TSS	Hela-S3	cervix
47	chr7:112578800-112580400	Active TSS	HSMM	muscle
48	chr7:112578800-112580400	Active TSS	NHDF-Ad	bronchial
49	chr7:112578800-112580600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:112578800-112580600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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