Variant report

Variant	rs1022312
Chromosome Location	chr2:10040351-10040352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10033449..10037613-chr2:10038043..10042119,5	MCF-7	breast:
2	chr2:10039201..10042198-chr2:10045779..10048080,2	MCF-7	breast:
3	chr2:9948070..9949733-chr2:10038866..10041132,2	K562	blood:
4	chr2:10037952..10040907-chr2:10047681..10050214,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10495576	0.84[CEU][hapmap]
rs1054561	0.84[CEU][hapmap];0.92[MEX][hapmap]
rs1054565	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs10803709	0.80[CEU][hapmap]
rs11677649	0.81[AMR][1000 genomes]
rs11686239	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12185679	0.84[CEU][hapmap]
rs12468764	0.80[CEU][hapmap];0.92[MEX][hapmap]
rs12479251	0.83[CEU][hapmap]
rs12614753	0.84[CEU][hapmap]
rs12615461	0.84[CEU][hapmap]
rs12617033	0.83[CEU][hapmap]
rs12621371	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs12991584	0.84[CEU][hapmap]
rs12995394	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs13002884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1367385	0.84[CEU][hapmap];0.87[MEX][hapmap]
rs16867210	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16867226	0.84[CEU][hapmap];0.92[MEX][hapmap]
rs16867240	0.82[CEU][hapmap]
rs1820965	0.92[MEX][hapmap]
rs1835426	0.84[CEU][hapmap]
rs1965411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971101	0.82[ASW][hapmap]
rs2052948	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163337	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241665	0.84[CEU][hapmap]
rs2245344	0.81[ASW][hapmap]
rs2303921	0.82[ASW][hapmap]
rs2357391	0.92[MEX][hapmap]
rs34577787	0.80[CEU][hapmap];0.92[MEX][hapmap]
rs35390016	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35466574	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35686192	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372222	0.83[CEU][hapmap]
rs3815977	0.84[CEU][hapmap]
rs445742	0.84[CEU][hapmap]
rs450085	0.83[CEU][hapmap]
rs4668650	0.84[CEU][hapmap]
rs4668654	0.80[CEU][hapmap];0.92[MEX][hapmap]
rs4669487	0.82[CEU][hapmap]
rs4669490	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs4669492	0.84[CEU][hapmap];0.92[MEX][hapmap]
rs4669493	0.84[CEU][hapmap];0.87[MEX][hapmap]
rs4669497	0.82[CEU][hapmap]
rs514905	0.84[CEU][hapmap]
rs57046626	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432041	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6707700	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707887	0.84[CEU][hapmap];0.92[MEX][hapmap]
rs6742427	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs6748720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv873632	chr2:10000978-10045014	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv1009210	chr2:10030072-10052257	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1006533	chr2:10030964-10065624	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1004743	chr2:10031389-10065624	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1022312	ATPBD4	trans	parietal	SCAN
rs1022312	TAF1B	cis	parietal	SCAN
rs1022312	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs1022312	TAF1B	cis	lymphoblastoid	seeQTL
rs1022312	TAF1B	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:9999200-10053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:10014800-10045400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
5	chr2:10024400-10053800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:10024800-10047600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:10024800-10051400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:10025000-10047000	Weak transcription	Thymus	Thymus
9	chr2:10025000-10053800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:10025000-10053800	Weak transcription	Ovary	ovary
11	chr2:10025000-10054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:10025000-10054400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:10025000-10054400	Weak transcription	Spleen	Spleen
14	chr2:10025400-10052600	Weak transcription	Left Ventricle	heart
15	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:10027000-10040400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:10027000-10047000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:10027400-10052200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:10027400-10053400	Weak transcription	Fetal Brain Male	brain
20	chr2:10027600-10052000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:10028200-10051000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:10028200-10053800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
24	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:10032600-10044600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:10032800-10044400	Weak transcription	Dnd41	blood
27	chr2:10033000-10044000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:10033000-10044400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:10033000-10052800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:10033600-10041600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:10036400-10047800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:10036400-10052200	Weak transcription	Liver	Liver
34	chr2:10036600-10047600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:10036800-10051800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:10037000-10047400	Weak transcription	Fetal Intestine Large	intestine
39	chr2:10037200-10040400	Weak transcription	Placenta	Placenta
40	chr2:10037200-10044600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:10037200-10044600	Weak transcription	Fetal Thymus	thymus
42	chr2:10037200-10047200	Weak transcription	Primary T cells from cord blood	blood
43	chr2:10037200-10051800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:10037600-10046000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:10037800-10045600	Weak transcription	HepG2	liver
47	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:10038000-10045000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:10038000-10047000	Weak transcription	Fetal Intestine Small	intestine
50	chr2:10038000-10047000	Weak transcription	Fetal Muscle Leg	muscle

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