Variant report

Variant	rs2617186
Chromosome Location	chr12:31750910-31750911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31745091..31747743-chr12:31750901..31752442,2	K562	blood:
2	chr12:31741307..31745552-chr12:31748528..31751513,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL20-7	chr12:31750885-31751290	NONHSAT027562

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction
ENSG00000252390	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11051445	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11051457	0.81[AFR][1000 genomes]
rs1150944	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1150946	0.85[AFR][1000 genomes]
rs1150947	0.84[AFR][1000 genomes]
rs1150951	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs1150952	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs1150956	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs1150957	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs1150959	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1150960	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1150961	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs12302576	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12305954	0.86[AFR][1000 genomes]
rs12305966	1.00[CEU][hapmap]
rs1259215	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs1259237	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs1259240	0.81[AFR][1000 genomes]
rs1259358	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1259387	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs1259388	0.83[AFR][1000 genomes]
rs1259390	0.90[AFR][1000 genomes]
rs1259391	0.81[AFR][1000 genomes]
rs1259394	0.83[AFR][1000 genomes]
rs1259397	0.81[AFR][1000 genomes]
rs1259402	0.87[AFR][1000 genomes]
rs1259403	0.87[AFR][1000 genomes]
rs1259406	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs1259407	0.90[AFR][1000 genomes]
rs1259408	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1259410	0.90[AFR][1000 genomes]
rs1259411	0.90[AFR][1000 genomes]
rs1259412	0.90[AFR][1000 genomes]
rs1259416	0.90[AFR][1000 genomes]
rs1259421	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs1259424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259429	0.85[AFR][1000 genomes]
rs1259436	0.85[AFR][1000 genomes]
rs1259440	0.83[AFR][1000 genomes]
rs1262389	0.81[AFR][1000 genomes]
rs1262391	0.83[AFR][1000 genomes]
rs1267631	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs1267686	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1267688	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1267689	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs1270211	0.83[AFR][1000 genomes]
rs1271127	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs1271661	0.83[AFR][1000 genomes]
rs1271662	0.83[AFR][1000 genomes]
rs1273260	0.90[AFR][1000 genomes]
rs1533704	1.00[EUR][1000 genomes]
rs1623868	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1677142	0.95[EUR][1000 genomes]
rs1677155	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1677156	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1677182	0.90[AFR][1000 genomes]
rs1677188	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1677190	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs1677215	1.00[EUR][1000 genomes]
rs1716213	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864912	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs2568896	1.00[CEU][hapmap]
rs2604050	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2617179	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2617187	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617192	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs2617210	0.87[AFR][1000 genomes]
rs2679488	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs2679493	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs2679501	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2682461	0.90[AFR][1000 genomes]
rs2682682	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs2682683	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs2682690	0.81[AFR][1000 genomes]
rs478620	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs56244356	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs708198	1.00[CEU][hapmap]
rs708199	1.00[CEU][hapmap]
rs708207	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs708211	1.00[CEU][hapmap]
rs7302818	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs793147	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs793152	1.00[CEU][hapmap]
rs793159	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs793172	0.83[AFR][1000 genomes]
rs793178	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs793183	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs793188	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs811088	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs971294	0.81[AFR][1000 genomes]
rs973510	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1840310	chr12:31743194-31750986	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv975472	chr12:31748491-31751020	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31745400-31760400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:31750200-31751600	Enhancers	Primary B cells from cord blood	blood
3	chr12:31750200-31758000	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:31750400-31751000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:31750600-31751200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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