Variant report

Variant	rs2039971
Chromosome Location	chr9:21815166-21815167
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:21813976..21815531-chr9:22227768..22230145,2	MCF-7	breast:
2	chr9:21815119..21818552-chr9:22084345..22087438,5	MCF-7	breast:
3	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
4	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
5	chr9:21815068..21816842-chr9:22213097..22214603,2	MCF-7	breast:
6	chr9:21814593..21817244-chr9:22101346..22103643,2	MCF-7	breast:
7	chr9:21813352..21815256-chr9:22105449..22107592,2	MCF-7	breast:
8	chr9:21814236..21815756-chr9:21816687..21818774,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000147889	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000240498	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10217131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10217379	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10429489	0.83[ASN][1000 genomes]
rs10511698	0.87[ASN][1000 genomes]
rs10511699	0.87[ASN][1000 genomes]
rs10511700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10757256	0.81[ASN][1000 genomes]
rs10811616	0.81[ASN][1000 genomes]
rs10811619	0.87[ASN][1000 genomes]
rs10811631	0.85[JPT][hapmap]
rs12002238	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12002663	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12004745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12336678	0.82[ASN][1000 genomes]
rs12336734	0.82[ASN][1000 genomes]
rs12337510	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12340988	0.87[ASN][1000 genomes]
rs12379110	0.85[ASN][1000 genomes]
rs12380373	0.85[ASN][1000 genomes]
rs13286524	0.87[ASN][1000 genomes]
rs13302653	0.92[JPT][hapmap]
rs2282245	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2383184	0.86[ASN][1000 genomes]
rs35235093	0.84[ASN][1000 genomes]
rs35526535	0.83[ASN][1000 genomes]
rs3931609	0.80[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs41517746	0.86[MEX][hapmap]
rs4326466	0.81[ASN][1000 genomes]
rs4375086	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4543632	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs55656405	0.83[ASN][1000 genomes]
rs56005066	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56237731	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56339876	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58495931	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59990401	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61258965	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6475580	0.81[ASN][1000 genomes]
rs6475581	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs6475582	0.86[ASN][1000 genomes]
rs6475583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6475584	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs66506556	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66587337	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67134687	0.80[AMR][1000 genomes]
rs67220270	0.89[ASN][1000 genomes]
rs7022981	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7029287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7033148	0.87[ASN][1000 genomes]
rs7037277	0.87[ASN][1000 genomes]
rs7040895	0.81[ASN][1000 genomes]
rs7042728	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs7048433	0.82[ASN][1000 genomes]
rs7851125	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7856455	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7859886	0.89[ASN][1000 genomes]
rs7860126	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7866860	0.87[ASN][1000 genomes]
rs7867176	0.80[CHD][hapmap]
rs7868246	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7869680	0.85[ASN][1000 genomes]
rs7871127	0.86[MEX][hapmap]
rs7871477	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7871631	0.83[ASN][1000 genomes]
rs7874112	0.92[JPT][hapmap];0.87[MEX][hapmap]
rs885518	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9298826	0.87[ASN][1000 genomes]
rs935054	0.89[ASN][1000 genomes]
rs945263	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:21804400-21816000	Weak transcription	Fetal Kidney	kidney
4	chr9:21805000-21816200	Weak transcription	Fetal Brain Male	brain
5	chr9:21806000-21817600	Genic enhancers	HMEC	breast
6	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:21806600-21815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:21806800-21815800	Weak transcription	Brain Germinal Matrix	brain
10	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
11	chr9:21811000-21815600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:21811600-21815600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:21811600-21815800	Weak transcription	Fetal Brain Female	brain
14	chr9:21812000-21815600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:21812000-21815600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:21812200-21815600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:21812200-21815600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:21812200-21815600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:21812200-21815600	Weak transcription	Aorta	Aorta
20	chr9:21812200-21815600	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:21812200-21815600	Weak transcription	Gastric	stomach
22	chr9:21812200-21815600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:21812200-21815800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:21812200-21815800	Weak transcription	Thymus	Thymus
25	chr9:21812200-21816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:21812200-21817000	Weak transcription	Fetal Intestine Small	intestine
27	chr9:21812200-21817200	Weak transcription	Esophagus	oesophagus
28	chr9:21812200-21817400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:21812400-21815400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:21812400-21815600	Weak transcription	Fetal Lung	lung
31	chr9:21812600-21815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:21812600-21815800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:21812800-21815600	Weak transcription	Fetal Stomach	stomach
34	chr9:21812800-21817400	Weak transcription	Right Ventricle	heart
35	chr9:21813200-21815400	Enhancers	Liver	Liver
36	chr9:21813200-21815600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:21813400-21815800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:21813400-21816000	Weak transcription	Spleen	Spleen
39	chr9:21813600-21815600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:21813600-21815600	Weak transcription	Psoas Muscle	Psoas
41	chr9:21813600-21815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:21813600-21817000	Weak transcription	Colonic Mucosa	Colon
43	chr9:21813800-21815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:21813800-21815600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:21813800-21815600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:21813800-21815600	Weak transcription	Placenta	Placenta
47	chr9:21813800-21815600	Weak transcription	Fetal Thymus	thymus
48	chr9:21813800-21815600	Weak transcription	Left Ventricle	heart
49	chr9:21813800-21815600	Weak transcription	Ovary	ovary
50	chr9:21813800-21815800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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