Variant report

Variant	rs2274459
Chromosome Location	chr6:33762242-33762243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 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	chr6:33750065..33752378-chr6:33760799..33763522,2	MCF-7	breast:
6	chr6:33760609..33762790-chr6:33764065..33767376,3	K562	blood:
7	chr6:33761243..33763447-chr6:33764378..33766723,2	MCF-7	breast:
8	chr6:33699067..33701380-chr6:33760767..33763233,2	MCF-7	breast:
9	chr6:33759914..33762466-chr6:33790813..33792897,2	MCF-7	breast:
10	chr6:33756053..33759472-chr6:33760488..33763867,4	MCF-7	breast:
11	chr6:33760837..33764079-chr6:33785814..33788727,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10456075	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10456420	1.00[EUR][1000 genomes]
rs10456421	0.93[EUR][1000 genomes]
rs10947432	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs10947441	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs12153877	0.98[EUR][1000 genomes]
rs12189725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12192035	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12192087	0.92[EUR][1000 genomes]
rs12193658	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12195409	1.00[EUR][1000 genomes]
rs12198383	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs12199132	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203688	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs12204620	1.00[EUR][1000 genomes]
rs12204992	1.00[EUR][1000 genomes]
rs12205398	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12211490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211565	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]
rs12660955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661400	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12662447	0.85[EUR][1000 genomes]
rs13200063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203745	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13204162	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13206228	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207666	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	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2281831	0.81[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs2281917	0.85[JPT][hapmap]
rs2281918	1.00[ASW][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap]
rs2281919	0.85[JPT][hapmap];0.87[TSI][hapmap]
rs2296749	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139049	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34339105	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34460651	0.99[EUR][1000 genomes]
rs34472165	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869648	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34884883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35274562	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	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	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35797388	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964955	0.83[EUR][1000 genomes]
rs36122085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793080	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3806107	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3818532	1.00[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap]
rs66617522	0.94[EUR][1000 genomes]
rs66670017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68168863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925337	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs729376	1.00[CEU][hapmap];1.00[JPT][hapmap];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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296097	0.85[JPT][hapmap];0.87[TSI][hapmap]
rs9469554	0.91[MKK][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Obesity (extreme)	19553259	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2274459	LEMD2	cis	parietal	SCAN
rs2274459	C6orf125	cis	cerebellum	SCAN
rs2274459	C6orf227	cis	parietal	SCAN
rs2274459	LEMD2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757600-33762400	Weak transcription	A549	lung
2	chr6:33757600-33763600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
4	chr6:33758000-33762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:33758400-33763600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:33759000-33762800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:33759000-33765600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:33759200-33763600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:33759400-33762600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33759400-33762600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:33759400-33762800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:33759600-33762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:33760000-33762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:33760400-33763600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:33760400-33763600	Bivalent Enhancer	HepG2	liver
16	chr6:33760600-33763600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:33760800-33762600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:33761400-33762400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:33761400-33762400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:33761600-33762600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:33761600-33763200	Enhancers	Fetal Intestine Large	intestine
22	chr6:33761800-33762800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:33762000-33762600	Bivalent Enhancer	Fetal Stomach	stomach
24	chr6:33762000-33763600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr6:33762000-33763600	Enhancers	Duodenum Mucosa	Duodenum
26	chr6:33762000-33763600	Enhancers	Fetal Intestine Small	intestine
27	chr6:33762000-33766800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:33762200-33763000	Enhancers	Fetal Lung	lung
29	chr6:33762200-33763400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:33762200-33763600	Enhancers	HUES64 Cell Line	embryonic stem cell

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