Variant report

Variant	rs1556516
Chromosome Location	chr9:22100176-22100177
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:22078947..22090885-chr9:22096375..22111093,52	MCF-7	breast:
2	chr9:22080093..22089919-chr9:22099951..22109614,29	MCF-7	breast:
3	chr9:22098016..22100676-chr9:22106122..22109084,4	MCF-7	breast:
4	chr9:21810090..21812748-chr9:22099940..22102610,2	MCF-7	breast:
5	chr9:21834703..21838145-chr9:22099294..22103119,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229298	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1004638	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10116277	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10217586	0.82[EUR][1000 genomes]
rs10511701	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10733376	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10738606	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738608	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10738609	0.92[EUR][1000 genomes]
rs10738610	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10757271	0.82[AMR][1000 genomes]
rs10757272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757273	0.91[ASN][1000 genomes]
rs10757274	0.96[EUR][1000 genomes]
rs10757275	0.95[EUR][1000 genomes]
rs10757277	0.89[EUR][1000 genomes]
rs10757278	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10757279	0.89[EUR][1000 genomes]
rs10811652	0.82[AMR][1000 genomes]
rs10811653	0.81[EUR][1000 genomes]
rs10811654	0.92[EUR][1000 genomes]
rs10811656	0.86[EUR][1000 genomes]
rs1333042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1333043	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1333046	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1333047	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1333048	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs1333049	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs1412834	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537370	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1537371	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537374	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1537375	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1537376	0.94[EUR][1000 genomes]
rs1970112	0.86[EUR][1000 genomes]
rs2210538	0.84[EUR][1000 genomes]
rs2383206	0.94[EUR][1000 genomes]
rs2383207	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2891168	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4977574	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4977575	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4977757	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6475606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475609	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341786	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341791	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7857118	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7857345	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs7859362	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs944797	0.94[EUR][1000 genomes]
rs9644860	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22097200-22105400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:22097400-22101800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:22097800-22101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:22097800-22101800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:22097800-22102000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:22097800-22102400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:22097800-22102600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:22097800-22105400	Weak transcription	Colonic Mucosa	Colon
9	chr9:22097800-22122400	Weak transcription	Dnd41	blood
10	chr9:22098000-22101800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:22098000-22101800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:22098000-22101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:22098000-22102200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:22098000-22102200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:22098000-22102200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:22098000-22104200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:22098000-22107600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:22098800-22101600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:22099000-22101800	Weak transcription	NHLF	lung
20	chr9:22099000-22102000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:22099200-22101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:22099200-22102000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:22099200-22102000	Weak transcription	NH-A	brain
24	chr9:22099200-22102800	Weak transcription	Psoas Muscle	Psoas
25	chr9:22099400-22101600	Weak transcription	Fetal Intestine Large	intestine
26	chr9:22099400-22101800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:22099400-22101800	Weak transcription	Placenta	Placenta
28	chr9:22099400-22101800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr9:22099400-22101800	Weak transcription	HMEC	breast
30	chr9:22099400-22101800	Weak transcription	HSMM	muscle
31	chr9:22099400-22101800	Weak transcription	HSMMtube	muscle
32	chr9:22099400-22101800	Weak transcription	NHDF-Ad	bronchial
33	chr9:22099400-22101800	Weak transcription	NHEK	skin
34	chr9:22099400-22102200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:22099400-22102400	Weak transcription	Osteobl	bone
36	chr9:22099400-22102800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:22099400-22107200	Weak transcription	Small Intestine	intestine
38	chr9:22099600-22101600	Weak transcription	Fetal Intestine Small	intestine
39	chr9:22099600-22101800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:22099600-22101800	Weak transcription	Hela-S3	cervix
41	chr9:22099600-22102400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:22099600-22102800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:22099600-22104000	Weak transcription	Adipose Nuclei	Adipose
44	chr9:22099800-22102400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:22099800-22102400	Weak transcription	Stomach Mucosa	stomach

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