Variant report

Variant	rs2282245
Chromosome Location	chr9:21815797-21815798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr9:21815606-21816002	GM12878	blood:	n/a	chr9:21815797-21815808
2	BCL11A	chr9:21815704-21815976	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:21800813..21805862-chr9:21815237..21818014,5	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:

Variant related genes	Relation type
TUBB8P1	TF binding region
ENSG00000099810	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000240498	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10217131	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217379	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10429489	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10511700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10757256	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10811609	0.80[ASN][1000 genomes]
rs10811616	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10811619	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10811631	0.85[JPT][hapmap]
rs10965124	0.87[ASN][1000 genomes]
rs10965131	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10965157	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10965158	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12002238	0.84[ASN][1000 genomes]
rs12002663	0.90[ASN][1000 genomes]
rs12004745	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12336678	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336734	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12337510	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12340988	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12348845	0.87[ASN][1000 genomes]
rs12379110	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12380313	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12380373	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13286524	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13302653	0.83[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1414258	0.85[ASN][1000 genomes]
rs1414259	0.85[ASN][1000 genomes]
rs1440992	0.87[ASN][1000 genomes]
rs2039971	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35235093	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35526535	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3802393	0.82[MEX][hapmap]
rs3931609	0.83[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4295749	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4326466	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4375086	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4399022	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4543632	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs55656405	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56005066	0.84[ASN][1000 genomes]
rs56237731	0.83[ASN][1000 genomes]
rs56339876	0.83[ASN][1000 genomes]
rs58495931	0.84[ASN][1000 genomes]
rs59990401	0.86[ASN][1000 genomes]
rs61258965	0.84[ASN][1000 genomes]
rs6475575	0.85[ASN][1000 genomes]
rs6475580	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475581	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475582	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6475583	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475584	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475588	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6475589	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66506556	0.81[ASN][1000 genomes]
rs66587337	0.85[ASN][1000 genomes]
rs67220270	0.81[ASN][1000 genomes]
rs7022981	0.81[ASN][1000 genomes]
rs7029287	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7033148	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7040432	0.87[ASN][1000 genomes]
rs7040895	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041509	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7042728	0.83[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7042884	0.85[ASN][1000 genomes]
rs7850447	0.81[ASN][1000 genomes]
rs7851125	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859886	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860126	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866362	0.85[ASN][1000 genomes]
rs7866533	0.85[ASN][1000 genomes]
rs7866860	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867176	0.83[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7868246	0.82[ASN][1000 genomes]
rs7868253	0.84[ASN][1000 genomes]
rs7869680	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871477	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871631	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7874112	0.83[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs885518	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298826	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs935054	0.81[ASN][1000 genomes]
rs945263	0.83[EUR][1000 genomes];0.90[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2282245	KIAA1797	cis	parietal	SCAN

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	chr9:21811600-21815800	Weak transcription	Fetal Brain Female	brain
12	chr9:21812200-21815800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:21812200-21815800	Weak transcription	Thymus	Thymus
14	chr9:21812200-21816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:21812200-21817000	Weak transcription	Fetal Intestine Small	intestine
16	chr9:21812200-21817200	Weak transcription	Esophagus	oesophagus
17	chr9:21812200-21817400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:21812600-21815800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:21812800-21817400	Weak transcription	Right Ventricle	heart
20	chr9:21813400-21815800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:21813400-21816000	Weak transcription	Spleen	Spleen
22	chr9:21813600-21815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:21813600-21817000	Weak transcription	Colonic Mucosa	Colon
24	chr9:21813800-21815800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:21813800-21815800	Weak transcription	HUVEC	blood vessel
26	chr9:21813800-21816000	Weak transcription	Lung	lung
27	chr9:21813800-21816000	Weak transcription	Pancreas	Pancrea
28	chr9:21813800-21817400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:21814000-21815800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr9:21814000-21815800	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:21814000-21815800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr9:21814000-21815800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:21814000-21816000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:21814000-21817200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:21814000-21817400	Weak transcription	Right Atrium	heart
36	chr9:21814000-21831800	Weak transcription	Fetal Heart	heart
37	chr9:21814200-21815800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:21814200-21815800	Weak transcription	Primary B cells from cord blood	blood
39	chr9:21814200-21815800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:21814200-21815800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:21814400-21815800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr9:21814400-21815800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr9:21814400-21815800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:21814400-21815800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr9:21814400-21815800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:21814400-21815800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:21814400-21816000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:21814400-21817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:21814400-21831800	Weak transcription	Stomach Mucosa	stomach
50	chr9:21814400-21837400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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