Variant report

Variant	rs1372108
Chromosome Location	chr11:70965076-70965077
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	EP300	chr11:70964361-70965127	T-47D	breast:	n/a	chr11:70965090-70965103
2	SP1	chr11:70963735-70965234	A549	lung:	n/a	chr11:70964191-70964201 chr11:70963868-70963877 chr11:70964320-70964329 chr11:70963869-70963878 chr11:70964190-70964202 chr11:70963868-70963877 chr11:70964317-70964324 chr11:70963869-70963882 chr11:70963867-70963879 chr11:70964187-70964201 chr11:70964318-70964330 chr11:70963867-70963879 chr11:70964191-70964200 chr11:70964190-70964202 chr11:70964318-70964330
3	HDAC2	chr11:70963504-70965103	HepG2	liver:	n/a	chr11:70964766-70964780
4	GATA3	chr11:70964241-70965137	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr11:70962876-70965150	MCF-7	breast:	n/a	n/a
6	MYBL2	chr11:70963887-70965198	HepG2	liver:	n/a	n/a
7	MAZ	chr11:70962302-70965186	IMR90	lung:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70962364-70962373 chr11:70963660-70963670
8	REST	chr11:70964049-70965130	A549	lung:	n/a	chr11:70964527-70964541
9	EP300	chr11:70963434-70965236	HepG2	liver:	n/a	chr11:70965090-70965103
10	TCF12	chr11:70963631-70965358	A549	lung:	n/a	chr11:70964161-70964168 chr11:70963983-70963990 chr11:70964162-70964172
11	EP300	chr11:70964207-70965236	A549	lung:	n/a	chr11:70965090-70965103
12	ARID3A	chr11:70963859-70965117	HepG2	liver:	n/a	n/a
13	ZEB1	chr11:70962810-70965218	HepG2	liver:	n/a	chr11:70963524-70963533 chr11:70963464-70963473 chr11:70963466-70963473
14	FOXA2	chr11:70965011-70965275	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:70963635..70965716-chr11:71014557..71017556,4	MCF-7	breast:
2	chr11:70856232..70858594-chr11:70962827..70965344,2	MCF-7	breast:
3	chr11:70964631..70967920-chr11:70993690..70996752,4	MCF-7	breast:
4	chr11:70962835..70965130-chr5:139026152..139027857,2	MCF-7	breast:

Variant related genes	Relation type
SHANK2	TF binding region
ENSG00000171604	Chromatin interaction
ENSG00000162105	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1004872	1.00[ASN][1000 genomes]
rs11603698	1.00[CEU][hapmap]
rs1985681	1.00[ASN][1000 genomes]
rs2919720	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2919726	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2919727	1.00[ASN][1000 genomes]
rs2919728	1.00[ASN][1000 genomes]
rs2919729	1.00[ASN][1000 genomes]
rs2919736	0.87[AMR][1000 genomes]
rs2919740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2919742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3020025	1.00[ASN][1000 genomes]
rs3020027	1.00[ASN][1000 genomes]
rs3020028	1.00[ASN][1000 genomes]
rs3020032	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3133512	1.00[CEU][hapmap]
rs4078937	0.89[ASN][1000 genomes]
rs60796828	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:70963400-70965600	Bivalent Enhancer	Fetal Lung	lung
2	chr11:70964200-70965600	Enhancers	Lung	lung
3	chr11:70964400-70965200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:70964400-70965200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:70964400-70966000	Bivalent Enhancer	Placenta	Placenta
6	chr11:70964400-70966800	Enhancers	Stomach Mucosa	stomach
7	chr11:70964400-70967400	Enhancers	Pancreas	Pancrea
8	chr11:70964600-70965200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
9	chr11:70964600-70965200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:70964600-70965400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr11:70964600-70965400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:70964600-70965400	Enhancers	Fetal Kidney	kidney
13	chr11:70964600-70965600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:70964600-70966200	Enhancers	Fetal Intestine Large	intestine
15	chr11:70964600-70966400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:70964600-70966400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:70964600-70966600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:70964600-70966600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:70964600-70967200	Enhancers	Fetal Intestine Small	intestine
20	chr11:70964600-70967400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr11:70964800-70965200	Flanking Active TSS	A549	lung
22	chr11:70964800-70965400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr11:70964800-70965400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr11:70964800-70965400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
25	chr11:70964800-70965400	Flanking Active TSS	HepG2	liver
26	chr11:70965000-70965400	Enhancers	Liver	Liver
27	chr11:70965000-70965600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:70965000-70965600	Enhancers	Gastric	stomach
29	chr11:70965000-70965800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr11:70965000-70965800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:70965000-70966200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
32	chr11:70965000-70967600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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