Variant report

Variant	rs6479426
Chromosome Location	chr9:95382641-95382642
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	POLR2A	chr9:95382425-95382674	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:95381571-95382831	HL-60	blood:	n/a	n/a
3	POLR2A	chr9:95381765-95382956	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:95382291-95383005	K562	blood:	n/a	n/a
5	POLR2A	chr9:95382577-95382679	K562	blood:	n/a	n/a
6	POLR2A	chr9:95382582-95382672	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95379288..95383213-chr9:95431051..95434876,7	MCF-7	breast:
2	chr9:95381141..95382834-chr9:95399062..95400590,2	MCF-7	breast:
3	chr9:95371374..95373769-chr9:95381769..95384696,2	K562	blood:

Variant related genes	Relation type
IPPK	TF binding region
ENSG00000188312	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10491806	0.91[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs10820997	0.84[MEX][hapmap]
rs10820998	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs10821009	0.84[MEX][hapmap]
rs10821012	0.83[MEX][hapmap]
rs10992367	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs10992380	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs10992382	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992384	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992390	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs10992392	0.91[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs10992394	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992404	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992406	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992407	0.88[CHB][hapmap]
rs10992408	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs10992414	0.88[CHB][hapmap]
rs10992426	0.85[AMR][1000 genomes]
rs10992433	0.85[AMR][1000 genomes]
rs10992434	0.84[MEX][hapmap]
rs10992444	0.84[MEX][hapmap]
rs10992445	0.84[MEX][hapmap]
rs10992448	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10992453	0.88[CHB][hapmap]
rs10992460	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10992461	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs1117670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236013	0.81[AMR][1000 genomes]
rs12236754	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs12237216	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12238691	0.88[CHB][hapmap]
rs12685080	0.81[YRI][hapmap]
rs12685257	0.84[MEX][hapmap]
rs12685780	0.84[MEX][hapmap]
rs12686780	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12686781	0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1323523	0.91[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes]
rs1326775	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1407944	0.88[AMR][1000 genomes]
rs1552908	0.85[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1575460	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17366488	0.81[AMR][1000 genomes]
rs1853468	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1874128	0.91[ASW][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1980705	0.83[ASW][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2038685	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2038686	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2088055	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2131919	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap]
rs2146848	0.91[CEU][hapmap]
rs2148537	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2181584	0.88[CHB][hapmap]
rs2274413	0.83[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2277166	0.83[AMR][1000 genomes]
rs2281888	0.83[ASW][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296080	0.84[MEX][hapmap]
rs3203916	0.84[MEX][hapmap]
rs3739605	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs41266683	0.84[AMR][1000 genomes]
rs556	0.84[MEX][hapmap]
rs58045868	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7031163	0.88[CHB][hapmap];0.96[MEX][hapmap]
rs7850075	0.91[MEX][hapmap]
rs7850871	0.83[AMR][1000 genomes]
rs7851947	0.88[AMR][1000 genomes]
rs7853617	0.80[AMR][1000 genomes]
rs7856147	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs7857105	0.91[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs7857502	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes]
rs7863882	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7863890	0.83[ASW][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs7864889	0.83[ASW][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7875050	0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs879812	0.83[ASW][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs912261	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs912264	0.91[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs971984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9775970	0.82[AMR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6479426	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs6479426	CENPP	cis	multi-tissue	Pritchard
rs6479426	C9orf89	cis	cerebellum	SCAN
rs6479426	ANKRD19	cis	cerebellum	SCAN
rs6479426	FBP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95363400-95396000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:95370600-95394000	Weak transcription	Psoas Muscle	Psoas
3	chr9:95371400-95398200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:95371800-95399000	Weak transcription	Aorta	Aorta
5	chr9:95371800-95407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:95372000-95394200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:95372400-95383400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:95372600-95383200	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:95372800-95382800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:95372800-95383000	Strong transcription	Fetal Brain Female	brain
11	chr9:95372800-95383200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:95372800-95384200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:95373000-95383000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:95373000-95383200	Strong transcription	Brain Hippocampus Middle	brain
15	chr9:95373000-95383400	Strong transcription	Brain Germinal Matrix	brain
16	chr9:95373000-95384200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:95373000-95384200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr9:95373000-95384200	Strong transcription	Primary T cells from cord blood	blood
19	chr9:95373000-95384200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:95373000-95384400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:95373000-95384800	Strong transcription	Dnd41	blood
22	chr9:95373000-95421200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr9:95373200-95382800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:95373200-95383200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr9:95373200-95383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:95373200-95384000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:95373200-95388000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr9:95373200-95399200	Weak transcription	Small Intestine	intestine
29	chr9:95373400-95383000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:95373600-95383400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:95373600-95383400	Strong transcription	Thymus	Thymus
32	chr9:95373800-95383400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr9:95373800-95384000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:95373800-95384400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:95374000-95383000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:95374000-95383200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr9:95374000-95383400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr9:95374000-95384400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:95374000-95394000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:95374200-95382800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:95374200-95384000	Strong transcription	GM12878-XiMat	blood
42	chr9:95374800-95384200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:95375000-95383000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:95375200-95405000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:95375400-95383200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:95375400-95383200	Strong transcription	NHEK	skin
47	chr9:95375400-95403000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:95375600-95383200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:95376400-95383400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr9:95376400-95384200	Enhancers	Ovary	ovary

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