Variant report

Variant	rs12195409
Chromosome Location	chr6:33757482-33757483
allele	C/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	YY1	chr6:33755711-33757699	SK-N-SH	brain:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
2	POLR2A	chr6:33755375-33757546	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:33755402-33757555	GM12892	blood:	n/a	n/a
4	CBX3	chr6:33756675-33757498	K562	blood:	n/a	n/a
5	POLR2A	chr6:33755608-33757706	HL-60	blood:	n/a	n/a
6	POLR2A	chr6:33754123-33757999	HUVEC	blood vessel:	n/a	n/a
7	YY1	chr6:33756225-33757612	K562	blood:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
8	MAX	chr6:33755692-33757692	HepG2	liver:	n/a	chr6:33756978-33756987
9	POLR2A	chr6:33754585-33758231	HepG2	liver:	n/a	n/a
10	EGR1	chr6:33756597-33757511	HCT-116	colon:	n/a	n/a
11	YY1	chr6:33756649-33757498	SK-N-SH	brain:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
12	YY1	chr6:33755941-33757702	K562	blood:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
13	YY1	chr6:33756698-33757501	NT2-D1	testis:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
14	POLR2A	chr6:33756519-33757753	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:33755766-33757599	GM12891	blood:	n/a	n/a
16	MXI1	chr6:33754826-33757645	IMR90	lung:	n/a	n/a
17	YY1	chr6:33756472-33757601	GM12891	blood:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
18	POLR2A	chr6:33757414-33757591	MCF-7	breast:	n/a	n/a
19	YY1	chr6:33756562-33757572	ECC-1	luminal epithelium:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
20	HCFC1	chr6:33754888-33757740	Hela-S3	cervix:	n/a	n/a
21	NR2F2	chr6:33756732-33757674	K562	blood:	n/a	n/a
22	POLR2A	chr6:33756489-33757684	GM12878	blood:	n/a	n/a
23	YY1	chr6:33756435-33757482	GM12892	blood:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
24	MXI1	chr6:33755276-33757747	SK-N-SH	brain:	n/a	n/a
25	YY1	chr6:33756442-33757543	H1-hESC	embryonic stem cell:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
26	POLR2A	chr6:33754909-33758028	IMR90	lung:	n/a	n/a
27	YY1	chr6:33756473-33757601	H1-hESC	embryonic stem cell:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
28	MTA3	chr6:33755260-33757493	GM12878	blood:	n/a	n/a
29	YY1	chr6:33755928-33757623	GM12878	blood:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
30	YY1	chr6:33755845-33757512	GM12892	blood:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
31	YY1	chr6:33755819-33757678	HepG2	liver:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
32	YY1	chr6:33756465-33757627	SK-N-SH_RA	brain:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
33	YY1	chr6:33755829-33757625	GM12878	blood:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
34	YY1	chr6:33756586-33757546	HCT-116	colon:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
35	YY1	chr6:33756690-33757520	HepG2	liver:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
36	CREB1	chr6:33755954-33757542	K562	blood:	n/a	n/a
37	YY1	chr6:33756404-33757619	SK-N-SH_RA	brain:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
38	YY1	chr6:33756496-33757508	ECC-1	luminal epithelium:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
39	REST	chr6:33755546-33757587	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr6:33754903-33758533	HUVEC	blood vessel:	n/a	n/a
41	JUND	chr6:33756736-33757530	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33677680..33679812-chr6:33755384..33758328,2	MCF-7	breast:
2	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
3	chr6:33756927..33758602-chr6:33764987..33767346,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10456420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456421	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947418	0.86[AFR][1000 genomes]
rs11755257	0.86[AFR][1000 genomes]
rs11757612	0.86[AFR][1000 genomes]
rs11758330	0.86[AFR][1000 genomes]
rs12153877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189725	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12192035	0.94[EUR][1000 genomes]
rs12192087	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193658	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198383	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199132	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12200154	0.86[AFR][1000 genomes]
rs12204620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205398	0.87[AFR][1000 genomes]
rs12211490	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12211554	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12211565	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12215329	0.93[EUR][1000 genomes]
rs12660955	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12662447	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200063	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs13206228	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13207666	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13213889	0.97[EUR][1000 genomes]
rs2274459	1.00[EUR][1000 genomes]
rs2296749	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34139049	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34339105	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34460651	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34472165	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34778247	1.00[ASN][1000 genomes]
rs34869648	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34884883	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35095444	0.91[ASN][1000 genomes]
rs35274562	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35328423	0.88[EUR][1000 genomes]
rs35366046	0.92[EUR][1000 genomes]
rs35445446	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646598	0.92[EUR][1000 genomes]
rs35721478	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35797388	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs35964955	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36122085	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3793080	0.97[EUR][1000 genomes]
rs3806107	0.97[EUR][1000 genomes]
rs3818532	1.00[ASN][1000 genomes]
rs66617522	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66670017	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs68168863	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6925337	0.94[EUR][1000 genomes]
rs71565393	0.86[AFR][1000 genomes]
rs72880510	0.91[ASN][1000 genomes]
rs729376	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs751095	1.00[EUR][1000 genomes]
rs755239	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs877187	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS 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	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33755800-33757600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33756000-33757600	Active TSS	NHLF	lung
3	chr6:33756200-33757600	Active TSS	Duodenum Mucosa	Duodenum
4	chr6:33757000-33757600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:33757000-33757600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:33757000-33757600	Enhancers	Placenta	Placenta
7	chr6:33757000-33757600	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr6:33757000-33757600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr6:33757000-33757600	Flanking Active TSS	Dnd41	blood
10	chr6:33757000-33757600	Flanking Active TSS	Hela-S3	cervix
11	chr6:33757000-33757600	Flanking Active TSS	HepG2	liver
12	chr6:33757000-33757600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:33757000-33757800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr6:33757000-33758000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:33757000-33758000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:33757000-33758800	Enhancers	Spleen	Spleen
17	chr6:33757000-33760000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:33757000-33760200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:33757200-33757600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:33757200-33757600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:33757200-33757600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:33757200-33757600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:33757200-33757600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:33757200-33757600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:33757200-33757600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:33757200-33757600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:33757200-33757600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:33757200-33757600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:33757200-33757600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:33757200-33757600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:33757200-33757600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:33757200-33757600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr6:33757200-33757600	Flanking Active TSS	Liver	Liver
34	chr6:33757200-33757600	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr6:33757200-33757600	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr6:33757200-33757600	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr6:33757200-33757600	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr6:33757200-33757600	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr6:33757200-33757600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr6:33757200-33757600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:33757200-33757600	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr6:33757200-33757600	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr6:33757200-33757600	Enhancers	Esophagus	oesophagus
44	chr6:33757200-33757600	Flanking Active TSS	Fetal Brain Female	brain
45	chr6:33757200-33757600	Flanking Active TSS	Right Ventricle	heart
46	chr6:33757200-33757600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:33757200-33757600	Flanking Active TSS	A549	lung
48	chr6:33757200-33757600	Flanking Active TSS	HSMM	muscle
49	chr6:33757200-33757600	Flanking Active TSS	HUVEC	blood vessel
50	chr6:33757200-33757600	Flanking Active TSS	NH-A	brain

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