Variant report

Variant	rs1980934
Chromosome Location	chr9:72361218-72361219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72286201..72287971-chr9:72360095..72361896,2	K562	blood:
2	chr9:72359106..72363474-chr9:72372322..72376083,7	MCF-7	breast:
3	chr9:72361031..72363861-chr9:72374055..72376198,2	MCF-7	breast:
4	chr9:72360748..72362784-chr9:72371625..72375303,3	K562	blood:
5	chr9:72360152..72362800-chr9:72364655..72369107,4	K562	blood:
6	chr9:72360551..72362642-chr9:72371189..72374048,2	K562	blood:
7	chr9:72360858..72363722-chr9:72367124..72369107,2	K562	blood:

Variant related genes	Relation type
ENSG00000188647	Chromatin interaction
ENSG00000107282	Chromatin interaction
ENSG00000261447	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10118222	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119846	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10217776	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10735560	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746706	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10746707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780610	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867922	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10868056	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11139996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330240	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1330332	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1411410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411413	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1536992	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1536994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1547690	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1576482	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1576483	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2026794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2150045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252130	0.94[ASN][1000 genomes]
rs2274745	0.98[ASN][1000 genomes]
rs2309531	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4535802	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535803	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023462	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037769	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7039383	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851707	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867543	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1048622	chr9:72303617-72371795	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72327800-72366800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:72333400-72374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:72337400-72366400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:72347000-72364600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:72347200-72361600	Weak transcription	Ovary	ovary
6	chr9:72347200-72364800	Weak transcription	Fetal Brain Female	brain
7	chr9:72347200-72371400	Weak transcription	Small Intestine	intestine
8	chr9:72347200-72373400	Weak transcription	Esophagus	oesophagus
9	chr9:72347200-72373400	Weak transcription	Fetal Intestine Small	intestine
10	chr9:72347200-72374200	Weak transcription	Spleen	Spleen
11	chr9:72347400-72361800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:72347400-72362200	Weak transcription	Aorta	Aorta
13	chr9:72347400-72374000	Weak transcription	Gastric	stomach
14	chr9:72347600-72362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:72347600-72362600	Weak transcription	Right Ventricle	heart
16	chr9:72347600-72368400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr9:72348200-72361800	Weak transcription	Fetal Brain Male	brain
18	chr9:72348400-72363800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:72348600-72364000	Weak transcription	Colonic Mucosa	Colon
20	chr9:72348800-72362000	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:72348800-72362200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:72348800-72362200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:72348800-72362400	Weak transcription	Lung	lung
24	chr9:72348800-72368600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:72348800-72373000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:72348800-72373000	Weak transcription	NHEK	skin
27	chr9:72348800-72373200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:72349000-72362200	Weak transcription	Brain Angular Gyrus	brain
29	chr9:72349200-72362000	Weak transcription	Thymus	Thymus
30	chr9:72349200-72363800	Weak transcription	NH-A	brain
31	chr9:72349600-72363800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:72350200-72363800	Weak transcription	HSMMtube	muscle
33	chr9:72352400-72362200	Weak transcription	Fetal Stomach	stomach
34	chr9:72352400-72365800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:72353400-72365800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:72353600-72362200	Weak transcription	Psoas Muscle	Psoas
37	chr9:72356400-72361400	Weak transcription	NHLF	lung
38	chr9:72356400-72361800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:72356600-72362000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr9:72356600-72364000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:72356800-72370000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr9:72358600-72363000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:72358800-72361400	Strong transcription	Fetal Intestine Large	intestine
44	chr9:72359000-72361400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:72359000-72361600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr9:72359000-72362800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:72359200-72361400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:72359200-72362000	Weak transcription	Fetal Heart	heart
49	chr9:72359400-72362200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:72359600-72361600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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