Variant report

Variant	rs12236825
Chromosome Location	chr9:97725433-97725434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97725333..97727926-chr9:97728619..97730960,2	MCF-7	breast:
2	chr9:97724167..97725875-chr9:97766269..97768051,2	MCF-7	breast:
3	chr9:97724206..97726133-chr9:97729459..97731665,2	MCF-7	breast:
4	chr9:97724594..97727372-chr9:97752153..97754740,2	K562	blood:
5	chr9:97723418..97725512-chr9:97771283..97773130,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10512250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993409	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993422	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993424	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993426	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993428	1.00[CHB][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993430	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993431	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993438	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993440	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993447	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993448	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993450	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236203	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238576	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16911886	0.91[CHB][hapmap]
rs16911887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802457	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56855628	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57054200	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58325577	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59246309	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59630616	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7023719	0.85[JPT][hapmap]
rs7848018	0.90[CHB][hapmap]
rs7857726	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7866661	0.90[CHB][hapmap]
rs7867908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7875287	0.86[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7875888	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97709200-97730400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:97713400-97726200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:97713800-97757400	Weak transcription	Fetal Brain Female	brain
5	chr9:97714200-97734200	Weak transcription	Lung	lung
6	chr9:97714200-97735800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:97715000-97735600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:97715000-97758200	Weak transcription	Spleen	Spleen
9	chr9:97715200-97732200	Weak transcription	Ovary	ovary
10	chr9:97715200-97734600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:97715200-97748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:97715400-97735800	Weak transcription	Right Ventricle	heart
13	chr9:97715400-97741200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
15	chr9:97715600-97730000	Weak transcription	Hela-S3	cervix
16	chr9:97715600-97742000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr9:97715600-97742000	Weak transcription	Psoas Muscle	Psoas
18	chr9:97715600-97742400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:97715800-97735600	Weak transcription	NHDF-Ad	bronchial
20	chr9:97716000-97729400	Weak transcription	Fetal Kidney	kidney
21	chr9:97716000-97735200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:97716000-97742400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:97716200-97734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:97716200-97734000	Weak transcription	Left Ventricle	heart
25	chr9:97716200-97735200	Weak transcription	NH-A	brain
26	chr9:97716200-97735400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:97716600-97734200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:97716600-97735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:97716800-97732400	Weak transcription	Fetal Heart	heart
30	chr9:97718800-97736800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:97718800-97744000	Weak transcription	GM12878-XiMat	blood
32	chr9:97719000-97730000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:97719000-97733400	Weak transcription	Primary B cells from cord blood	blood
34	chr9:97719000-97733800	Weak transcription	Aorta	Aorta
35	chr9:97719000-97734000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr9:97719000-97735600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:97719000-97735800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:97719000-97743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:97719000-97745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:97719200-97729600	Weak transcription	Fetal Intestine Small	intestine
41	chr9:97719200-97732600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:97719200-97732800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:97719200-97733800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:97719400-97726200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr9:97719400-97730000	Weak transcription	Fetal Intestine Large	intestine
46	chr9:97719400-97732200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:97719400-97735400	Weak transcription	Osteobl	bone
48	chr9:97719400-97735600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:97719400-97735800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:97719400-97737800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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