Variant report

Variant	rs12660955
Chromosome Location	chr6:33760320-33760321
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33760216-33760405	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33754496..33759383-chr6:33759533..33763241,9	K562	blood:
2	chr6:33760052..33762868-chr6:33807891..33810024,2	MCF-7	breast:
3	chr6:33710782..33712479-chr6:33760281..33762991,2	MCF-7	breast:
4	chr6:33759898..33762472-chr6:33773491..33776525,3	K562	blood:
5	chr6:33758412..33760501-chr6:33767524..33770306,2	MCF-7	breast:
6	chr6:33758565..33760342-chr6:33771227..33773397,2	MCF-7	breast:
7	chr6:33759914..33762466-chr6:33790813..33792897,2	MCF-7	breast:

No data

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000161904	Chromatin interaction
ENSG00000096395	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10456075	0.82[ASN][1000 genomes]
rs10456420	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10456421	0.93[EUR][1000 genomes]
rs10947418	0.86[AFR][1000 genomes]
rs10947432	0.82[ASN][1000 genomes]
rs11755257	0.86[AFR][1000 genomes]
rs11757612	0.86[AFR][1000 genomes]
rs11758330	0.86[AFR][1000 genomes]
rs12153877	0.98[EUR][1000 genomes]
rs12189725	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12192035	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12192087	0.92[EUR][1000 genomes]
rs12193658	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12195409	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12198383	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12199132	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12200154	0.86[AFR][1000 genomes]
rs12203688	0.88[ASN][1000 genomes]
rs12204620	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12204992	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12205398	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12211490	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211554	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211565	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215329	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661400	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12662447	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13200063	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204162	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13206228	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207666	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13213889	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13214874	0.82[ASN][1000 genomes]
rs2274459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281831	0.88[ASN][1000 genomes]
rs2296749	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139049	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34339105	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34460651	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs34472165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869648	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34884883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35274562	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35328423	0.88[EUR][1000 genomes]
rs35366046	0.92[EUR][1000 genomes]
rs35445446	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35646598	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35698850	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35721478	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35797388	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964955	0.83[EUR][1000 genomes]
rs36122085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793080	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3806107	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66617522	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs66670017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68168863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925337	0.94[EUR][1000 genomes]
rs71565393	0.86[AFR][1000 genomes]
rs729376	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751095	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877187	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757400-33761400	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr6:33757600-33760800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:33757600-33761000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:33757600-33762400	Weak transcription	A549	lung
5	chr6:33757600-33763600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
7	chr6:33758000-33762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:33758400-33763600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:33759000-33761000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:33759000-33762800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:33759000-33765600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:33759200-33763600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:33759400-33760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:33759400-33761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:33759400-33762200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:33759400-33762600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:33759400-33762600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:33759400-33762800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:33759600-33762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:33759800-33760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:33759800-33761600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr6:33760000-33760400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:33760000-33760400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:33760000-33762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:33760200-33760600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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