Variant report

Variant	rs1993912
Chromosome Location	chr9:5987781-5987782
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5986224..5990108-chr9:6007195..6009736,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263575	Chromatin interaction
ENSG00000183354	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10116214	1.00[ASN][1000 genomes]
rs10124484	1.00[CHB][hapmap]
rs10125832	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10975350	0.90[AFR][1000 genomes]
rs11793956	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12337300	0.92[AFR][1000 genomes]
rs12337445	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs12337790	1.00[CHB][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs12339886	0.84[MKK][hapmap]
rs12339889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12340531	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12341021	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12342282	0.85[CHD][hapmap];1.00[MEX][hapmap]
rs12343325	0.90[AFR][1000 genomes]
rs12345849	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12351533	0.88[AFR][1000 genomes]
rs12352918	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260130	1.00[MEX][hapmap]
rs1330124	1.00[CHB][hapmap]
rs1776008	1.00[MEX][hapmap]
rs2233177	0.85[CHD][hapmap]
rs2233178	0.85[CHD][hapmap]
rs2797512	1.00[MEX][hapmap]
rs380568	1.00[CHB][hapmap]
rs57154492	0.81[AMR][1000 genomes]
rs60037728	0.81[AMR][1000 genomes]
rs7029847	0.94[AFR][1000 genomes]
rs73383144	0.94[AFR][1000 genomes]
rs73387085	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	0.91[AMR][1000 genomes]
rs73639568	0.91[AMR][1000 genomes]
rs7853706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858084	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7859471	1.00[CHB][hapmap]
rs7875607	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5940000-6006800	Weak transcription	Gastric	stomach
2	chr9:5948000-6006000	Weak transcription	Right Ventricle	heart
3	chr9:5950600-6006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:5955000-5993600	Weak transcription	Lung	lung
5	chr9:5956200-5988000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:5957400-6004400	Weak transcription	Brain Germinal Matrix	brain
7	chr9:5957600-5991800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:5967000-5996600	Weak transcription	Brain Angular Gyrus	brain
9	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
10	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
11	chr9:5969200-5996800	Weak transcription	HMEC	breast
12	chr9:5969400-5999600	Weak transcription	HSMMtube	muscle
13	chr9:5972200-6005800	Weak transcription	NH-A	brain
14	chr9:5973600-5990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:5974000-5988200	Weak transcription	Fetal Intestine Small	intestine
16	chr9:5974000-5989000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:5974000-5990800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:5974000-5991400	Weak transcription	Esophagus	oesophagus
19	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:5974400-5999600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:5974800-5990600	Weak transcription	HepG2	liver
22	chr9:5974800-6001000	Weak transcription	Fetal Brain Female	brain
23	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
24	chr9:5977200-5989400	Weak transcription	HUVEC	blood vessel
25	chr9:5977200-5997000	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:5977400-5987800	Weak transcription	GM12878-XiMat	blood
27	chr9:5977400-5988400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:5977400-5993400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:5977400-5994400	Weak transcription	K562	blood
30	chr9:5977400-5996200	Weak transcription	Psoas Muscle	Psoas
31	chr9:5977400-5996600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:5977400-5996800	Weak transcription	Stomach Mucosa	stomach
33	chr9:5977400-6000800	Weak transcription	Small Intestine	intestine
34	chr9:5977400-6004800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:5977400-6005600	Weak transcription	NHLF	lung
36	chr9:5977400-6005800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
38	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
39	chr9:5978600-5988800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr9:5978800-5994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:5980000-5988600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr9:5980400-5988600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:5982600-5991200	Weak transcription	Aorta	Aorta
44	chr9:5982600-5995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:5982800-5993600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr9:5982800-5999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr9:5982800-6005200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:5983200-5993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:5983200-5993600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr9:5983200-5996800	Weak transcription	NHEK	skin

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