Variant report

Variant	rs7559505
Chromosome Location	chr2:64588987-64588988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64587517..64589977-chr2:64675091..64677835,2	MCF-7	breast:
2	chr2:64583701..64585384-chr2:64588386..64591287,2	MCF-7	breast:
3	chr2:64585285..64586792-chr2:64588668..64591328,2	MCF-7	breast:
4	chr2:64586053..64589004-chr2:64618647..64620148,2	MCF-7	breast:
5	chr2:64588315..64590489-chr2:64680621..64682875,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223935	Chromatin interaction
ENSG00000237217	Chromatin interaction
ENSG00000119862	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10164841	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206155	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1426704	0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4233932	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233933	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4300812	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4398260	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4459720	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476338	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4567922	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4671565	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671566	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546066	0.80[ASN][1000 genomes]
rs6720223	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6729384	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573704	0.93[ASN][1000 genomes]
rs7577604	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv874238	chr2:64575738-64614241	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64585400-64589800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:64586000-64591200	Enhancers	Esophagus	oesophagus
3	chr2:64586000-64591400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:64586400-64591000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:64586600-64589600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr2:64586600-64592800	Enhancers	Pancreas	Pancrea
7	chr2:64586800-64591000	Enhancers	Placenta	Placenta
8	chr2:64587000-64589000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr2:64587200-64590800	Enhancers	Stomach Mucosa	stomach
10	chr2:64587200-64591400	Enhancers	HMEC	breast
11	chr2:64587400-64591600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:64587400-64591800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:64587400-64593800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:64587600-64589000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:64587600-64589200	Weak transcription	Gastric	stomach
16	chr2:64587600-64590600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:64587600-64590800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:64587600-64590800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:64587600-64591200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:64587600-64591800	Enhancers	NHEK	skin
21	chr2:64587600-64595000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:64587600-64595200	Weak transcription	Right Atrium	heart
23	chr2:64587800-64589600	Weak transcription	Fetal Intestine Large	intestine
24	chr2:64587800-64591000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:64588000-64589000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:64588000-64589400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:64588000-64591200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:64588200-64589200	Weak transcription	Colonic Mucosa	Colon
29	chr2:64588400-64589400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:64588600-64589200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr2:64588800-64589000	Enhancers	Fetal Kidney	kidney
32	chr2:64588800-64589000	Enhancers	Fetal Muscle Leg	muscle
33	chr2:64588800-64590600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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