Variant report

Variant	rs6730262
Chromosome Location	chr2:64367694-64367695
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	CHD1	chr2:64366448-64368425	GM12878	blood:	n/a	n/a
2	ZNF384	chr2:64367378-64368306	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64360272..64363388-chr2:64364975..64368007,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225889	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10496107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472816	0.82[JPT][hapmap]
rs12477310	0.82[JPT][hapmap]
rs12479211	0.82[JPT][hapmap]
rs6733160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7349403	0.82[JPT][hapmap]
rs7573532	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6730262	PELI1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64340400-64370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:64347400-64368800	Weak transcription	Spleen	Spleen
3	chr2:64355400-64368800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:64356200-64368600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr2:64356400-64368200	Weak transcription	Brain Germinal Matrix	brain
6	chr2:64356400-64368800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:64357200-64368200	Weak transcription	Liver	Liver
8	chr2:64357200-64369600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:64359000-64368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:64359000-64368800	Weak transcription	Right Ventricle	heart
11	chr2:64359400-64368600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:64360600-64368800	Weak transcription	Fetal Stomach	stomach
13	chr2:64361400-64368800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:64361800-64370000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:64362200-64368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:64362400-64368000	Weak transcription	Fetal Lung	lung
17	chr2:64362400-64368800	Weak transcription	NH-A	brain
18	chr2:64362600-64368600	Enhancers	Primary T cells from cord blood	blood
19	chr2:64362600-64370000	Weak transcription	Ovary	ovary
20	chr2:64363200-64368800	Enhancers	Brain Substantia Nigra	brain
21	chr2:64363200-64368800	Enhancers	Colon Smooth Muscle	Colon
22	chr2:64363400-64368200	Weak transcription	Dnd41	blood
23	chr2:64363600-64368000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:64364000-64368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:64364000-64370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:64364000-64370400	Weak transcription	Lung	lung
27	chr2:64364400-64368600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:64364600-64367800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:64364600-64369200	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:64365000-64368800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:64365400-64368200	Weak transcription	Fetal Kidney	kidney
32	chr2:64365400-64370800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:64365600-64368000	Weak transcription	NHEK	skin
34	chr2:64365600-64368200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:64365600-64368600	Enhancers	Brain Hippocampus Middle	brain
36	chr2:64365600-64368800	Weak transcription	Hela-S3	cervix
37	chr2:64365600-64370000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:64365600-64370000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:64365600-64370000	Weak transcription	Placenta	Placenta
40	chr2:64365600-64370000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:64365800-64368000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:64365800-64368000	Weak transcription	Colonic Mucosa	Colon
43	chr2:64365800-64368600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:64365800-64368800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:64365800-64368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:64365800-64368800	Weak transcription	Small Intestine	intestine
47	chr2:64365800-64370200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:64365800-64370400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:64365800-64370400	Weak transcription	Esophagus	oesophagus
50	chr2:64366000-64367800	Weak transcription	K562	blood

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