Variant report

Variant	rs7101889
Chromosome Location	chr11:85595579-85595580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85589608..85591634-chr11:85594434..85597162,2	K562	blood:
2	chr11:85595243..85597275-chr11:85599038..85600664,2	MCF-7	breast:
3	chr11:85592798..85595721-chr11:85602697..85605651,2	MCF-7	breast:
4	chr11:85595576..85598404-chr11:85611809..85613970,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10501600	0.90[YRI][hapmap]
rs10501601	0.94[ASW][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap]
rs10898417	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11234452	0.80[EUR][1000 genomes]
rs11234454	0.80[YRI][hapmap]
rs11234457	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11234458	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11234462	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs11234463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11512932	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11826218	0.81[CEU][hapmap]
rs12271536	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12280977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12291381	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12361645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12361800	0.87[CEU][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap]
rs12363602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1445499	0.84[CEU][hapmap]
rs1445500	0.81[CEU][hapmap]
rs1445502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1445511	0.81[CEU][hapmap]
rs17148585	0.85[LWK][hapmap]
rs17744675	0.81[CEU][hapmap]
rs17744699	0.81[CEU][hapmap]
rs17744711	0.81[CEU][hapmap]
rs17817230	0.81[CEU][hapmap]
rs17817254	0.81[CEU][hapmap]
rs17817308	0.81[CEU][hapmap]
rs17817314	0.81[CEU][hapmap]
rs17817326	0.81[CEU][hapmap]
rs17817331	0.81[CEU][hapmap]
rs17817343	0.81[CEU][hapmap]
rs17817355	0.81[CEU][hapmap]
rs2044390	0.81[CEU][hapmap]
rs36093844	0.87[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4631905	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56160063	0.88[ASN][1000 genomes]
rs7108491	0.80[AFR][1000 genomes]
rs7113656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121363	0.81[CEU][hapmap]
rs7124956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7931771	0.80[CEU][hapmap]
rs7943104	0.81[CEU][hapmap]
rs895255	0.96[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv898051	chr11:85554057-85620823	Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv898052	chr11:85579304-85620823	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv898053	chr11:85579304-85634425	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7101889	SYTL2	cis	lymphoblastoid	seeQTL
rs7101889	SYTL2	cis	parietal	SCAN
rs7101889	PICALM	cis	cerebellum	SCAN
rs7101889	FZD4	cis	cerebellum	SCAN
rs7101889	SYTL2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85592800-85600400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:85595000-85596200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:85595000-85596400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:85595000-85597800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:85595000-85598200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:85595200-85595600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr11:85595200-85596000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:85595200-85596000	Enhancers	NHLF	lung
9	chr11:85595200-85598400	Enhancers	NHDF-Ad	bronchial
10	chr11:85595200-85598600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:85595400-85595600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr11:85595400-85595600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:85595400-85595600	Enhancers	Fetal Kidney	kidney
14	chr11:85595400-85595800	Enhancers	HSMMtube	muscle
15	chr11:85595400-85596000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:85595400-85596000	Enhancers	Hela-S3	cervix
17	chr11:85595400-85597600	Enhancers	Osteobl	bone

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