Variant report

Variant	rs11489598
Chromosome Location	chr7:101247430-101247431
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101242393..101247738-chr7:101456834..101460384,5	MCF-7	breast:
2	chr7:101207965..101209956-chr7:101246300..101248561,2	MCF-7	breast:
3	chr7:101245631..101247804-chr7:101249820..101253085,4	MCF-7	breast:
4	chr7:101244039..101255564-chr7:101454524..101463981,21	MCF-7	breast:
5	chr7:101239160..101242958-chr7:101243756..101248056,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11973739	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs12234788	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535019	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859621	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4727500	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv888821	chr7:101091470-101311540	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv831078	chr7:101094945-101257486	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv888822	chr7:101105017-101330734	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv888824	chr7:101109073-101330734	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv888825	chr7:101168283-101330734	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv888826	chr7:101230768-101277334	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11489598	PMPCB	cis	parietal	SCAN
rs11489598	TRIM4	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101242200-101249600	Weak transcription	Spleen	Spleen
2	chr7:101242400-101248400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:101242600-101248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:101242600-101248800	Weak transcription	Fetal Lung	lung
5	chr7:101242800-101251600	Weak transcription	Gastric	stomach
6	chr7:101245600-101250600	Enhancers	Placenta	Placenta
7	chr7:101246000-101248200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:101246400-101248600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:101246400-101251600	Weak transcription	Stomach Mucosa	stomach
10	chr7:101246400-101251800	Weak transcription	Pancreas	Pancrea
11	chr7:101246400-101252000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:101246400-101252000	Weak transcription	Fetal Intestine Small	intestine
13	chr7:101246600-101247800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:101246600-101247800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:101246600-101248400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:101246600-101248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:101246600-101249400	Weak transcription	HSMMtube	muscle
18	chr7:101246600-101251600	Weak transcription	HMEC	breast
19	chr7:101246600-101251800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:101246600-101252000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:101246800-101247800	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:101246800-101248800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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