Variant report

Variant	rs2894589
Chromosome Location	chr7:110663085-110663086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:110644466..110647207-chr7:110661227..110663752,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10215530	0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10274655	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10276691	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1029903	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953672	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953673	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953674	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11769641	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12671593	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12705748	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014855	0.80[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2058420	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2109863	0.94[CHB][hapmap]
rs2396301	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259016	0.80[ASN][1000 genomes]
rs259019	0.82[ASN][1000 genomes]
rs28505381	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28711130	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4727754	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730468	0.94[CHB][hapmap]
rs4730470	0.94[CHB][hapmap];0.81[MEX][hapmap]
rs4730471	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4730472	0.94[CHB][hapmap]
rs4730473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55921247	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466365	0.94[CHB][hapmap];0.81[MEX][hapmap]
rs6466366	0.94[CHB][hapmap]
rs6466371	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6965810	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs758953	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7782551	0.94[CHB][hapmap];0.81[MEX][hapmap]
rs7795011	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs7801774	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023596	chr7:109984459-110708071	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539061	chr7:109984459-110708071	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv531434	chr7:110310931-110839892	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3506497	chr7:110484691-111091738	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3506498	chr7:110484750-111091689	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv888973	chr7:110509579-110699652	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv2758129	chr7:110523298-110787849	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2759554	chr7:110523298-110787849	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1031546	chr7:110549137-110978256	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv817555	chr7:110564801-110990927	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1033286	chr7:110588021-110990928	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv539063	chr7:110588021-110990928	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv931978	chr7:110607590-111092490	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1025987	chr7:110609568-111258501	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv888975	chr7:110613685-110677656	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2830178	chr7:110645431-110778571	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1024477	chr7:110660006-110944477	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2894589	IMMP2L	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110648400-110663800	Weak transcription	Aorta	Aorta
2	chr7:110654200-110667000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:110657800-110666400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:110659600-110664400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr7:110659600-110664800	Weak transcription	HepG2	liver
6	chr7:110659600-110669400	Weak transcription	Fetal Lung	lung
7	chr7:110659800-110663200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr7:110659800-110664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:110659800-110669200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:110660000-110664200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:110660000-110664800	Enhancers	Primary T cells from cord blood	blood
12	chr7:110660000-110666000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:110660000-110669400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr7:110660200-110663600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:110660800-110669800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:110661800-110670600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr7:110662400-110664400	Enhancers	Dnd41	blood
18	chr7:110662400-110668000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr7:110662600-110663600	Weak transcription	Thymus	Thymus
20	chr7:110662800-110667400	Enhancers	Fetal Thymus	thymus
21	chr7:110663000-110664200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:110663000-110664400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:110663000-110664600	Enhancers	Primary T cells fromperipheralblood	blood

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