Variant report

Variant	rs1561957
Chromosome Location	chr9:100670272-100670273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100670192..100672522-chr9:100853837..100856499,2	K562	blood:
2	chr9:100667967..100674161-chr9:100680279..100686236,11	K562	blood:
3	chr9:100667726..100670333-chr9:100744534..100747383,2	MCF-7	breast:
4	chr9:100665233..100671095-chr9:100679720..100686341,8	MCF-7	breast:
5	chr9:100668446..100670680-chr9:100684264..100686164,2	MCF-7	breast:
6	chr9:100668512..100673720-chr9:100674176..100679549,8	K562	blood:
7	chr9:100662130..100664191-chr9:100669480..100671871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000201830	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1007506	0.80[CHB][hapmap]
rs10113884	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10115216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117642	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10119760	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119853	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10120412	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122541	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123699	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10512255	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512256	1.00[YRI][hapmap]
rs1059003	1.00[YRI][hapmap]
rs10739526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759975	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10760011	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818213	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10818241	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10984079	0.83[ASN][1000 genomes]
rs10984103	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10984134	0.83[ASN][1000 genomes]
rs10984156	0.83[ASN][1000 genomes]
rs10984195	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984218	0.87[ASN][1000 genomes]
rs10984222	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984230	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10984235	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984253	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984311	0.88[CHB][hapmap]
rs10984377	1.00[YRI][hapmap]
rs10984424	0.82[CHB][hapmap]
rs10984516	1.00[YRI][hapmap]
rs10984532	1.00[YRI][hapmap]
rs10984545	1.00[YRI][hapmap]
rs12004762	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343182	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12375612	1.00[YRI][hapmap]
rs12550872	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13286291	0.81[EUR][1000 genomes]
rs13287360	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13299924	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1348387	1.00[YRI][hapmap]
rs1443436	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687621	1.00[YRI][hapmap]
rs1947015	1.00[YRI][hapmap]
rs1955143	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2120264	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417575	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417576	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28417086	0.87[ASN][1000 genomes]
rs28697997	0.87[ASN][1000 genomes]
rs28703314	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3021525	0.85[ASN][1000 genomes]
rs35324451	0.82[EUR][1000 genomes]
rs3758250	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3808893	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808895	0.90[CHB][hapmap]
rs3824495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255258	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743139	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743142	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6478445	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6478469	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478471	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022148	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027221	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032086	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7032114	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034249	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034336	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034648	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036589	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037175	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038998	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042459	0.81[AMR][1000 genomes]
rs7044121	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7044799	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753537	0.91[ASN][1000 genomes]
rs7851498	1.00[YRI][hapmap]
rs7854948	1.00[YRI][hapmap]
rs7860144	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866436	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868534	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907581	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs925487	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9299258	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775370	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs993501	0.88[AMR][1000 genomes];0.92[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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1561957	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100656200-100670400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
3	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:100658600-100671600	Weak transcription	Ovary	ovary
6	chr9:100658600-100671600	Weak transcription	Small Intestine	intestine
7	chr9:100658600-100672200	Weak transcription	Esophagus	oesophagus
8	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:100660200-100671200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:100663000-100672200	Weak transcription	Colonic Mucosa	Colon
12	chr9:100663200-100671600	Weak transcription	HSMMtube	muscle
13	chr9:100663200-100671800	Weak transcription	NH-A	brain
14	chr9:100663200-100672000	Weak transcription	HepG2	liver
15	chr9:100663200-100672200	Weak transcription	HSMM	muscle
16	chr9:100663400-100671200	Weak transcription	Brain Angular Gyrus	brain
17	chr9:100663400-100671600	Weak transcription	NHDF-Ad	bronchial
18	chr9:100663400-100672600	Weak transcription	A549	lung
19	chr9:100663600-100671000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:100664000-100673200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:100664400-100672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:100665400-100671600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:100665600-100671000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:100665600-100671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:100665600-100678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:100665800-100671800	Weak transcription	HMEC	breast
28	chr9:100666200-100671600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:100666600-100675400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:100666600-100676000	Strong transcription	Fetal Intestine Large	intestine
31	chr9:100666800-100675800	Strong transcription	Fetal Stomach	stomach
32	chr9:100667000-100675800	Strong transcription	Fetal Intestine Small	intestine
33	chr9:100667200-100679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:100667400-100671000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:100667400-100671000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:100667400-100671600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:100667400-100671600	Weak transcription	NHEK	skin
39	chr9:100667400-100672200	Weak transcription	Fetal Lung	lung
40	chr9:100667600-100670400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr9:100667600-100671200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:100667600-100671800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr9:100667600-100672000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr9:100667800-100671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:100667800-100671600	Weak transcription	Osteobl	bone
46	chr9:100667800-100672200	Weak transcription	Psoas Muscle	Psoas
47	chr9:100667800-100674000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:100668000-100671600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:100668000-100672400	Weak transcription	Fetal Kidney	kidney
50	chr9:100668600-100670400	Genic enhancers	Thymus	Thymus

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