Variant report

Variant	rs10820997
Chromosome Location	chr9:95399321-95399322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95397145..95399782-chr9:95400372..95404536,5	K562	blood:
2	chr9:95396936..95399818-chr9:95416936..95418922,2	MCF-7	breast:
3	chr9:95381141..95382834-chr9:95399062..95400590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10820998	0.82[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs10821000	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10821009	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10821010	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10821012	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10992367	0.84[MEX][hapmap]
rs10992382	0.83[ASW][hapmap];0.84[MEX][hapmap]
rs10992384	0.83[ASW][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs10992390	0.82[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs10992392	0.83[ASW][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs10992402	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10992403	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10992406	0.86[JPT][hapmap]
rs10992407	0.82[JPT][hapmap]
rs10992408	0.86[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs10992409	0.81[AMR][1000 genomes]
rs10992413	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10992418	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992430	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10992431	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10992432	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10992434	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10992436	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10992442	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs10992443	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10992444	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10992445	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs10992448	0.84[MEX][hapmap]
rs10992451	0.80[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs10992460	0.84[MEX][hapmap]
rs10992461	0.84[MEX][hapmap]
rs10992469	0.86[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1117670	0.84[MEX][hapmap]
rs1125063	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1125064	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11535540	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12236013	0.83[AMR][1000 genomes]
rs12236393	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12236516	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12685080	0.86[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12685257	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs12685780	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs12685791	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12686780	0.82[AMR][1000 genomes]
rs12686781	0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs1323523	0.83[AMR][1000 genomes]
rs1326775	0.83[ASW][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs1552908	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs1555574	0.83[EUR][1000 genomes]
rs1575460	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs17366488	0.83[AMR][1000 genomes]
rs1810696	0.87[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs1853468	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs1874128	0.83[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs1980705	0.92[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2038685	0.80[AMR][1000 genomes]
rs2038686	0.83[AMR][1000 genomes]
rs2131919	0.84[MEX][hapmap]
rs2148537	0.83[ASW][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs2181586	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2274413	0.93[CEU][hapmap];0.93[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2277166	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2281888	0.92[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2296080	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs3203916	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs3739605	0.84[MEX][hapmap]
rs41266683	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs556	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs6479426	0.84[MEX][hapmap]
rs7031163	0.80[MEX][hapmap]
rs753802	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs753803	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs754600	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7853617	0.85[AMR][1000 genomes]
rs7856147	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857105	0.83[ASW][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs7857502	0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs7862106	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7863882	0.83[ASW][hapmap];0.84[MEX][hapmap]
rs7863890	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7864889	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7871537	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7875050	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8181065	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs879812	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs912261	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs912264	0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs971984	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs976320	0.81[CHB][hapmap];0.84[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10820997	OMD	cis	parietal	SCAN
rs10820997	BICD2	cis	brain	BrainEAC
rs10820997	BICD2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95371800-95407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:95373000-95421200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:95375200-95405000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:95375400-95403000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:95378200-95403600	Weak transcription	Fetal Brain Male	brain
6	chr9:95380800-95400600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:95380800-95429000	Weak transcription	Stomach Mucosa	stomach
8	chr9:95381400-95402800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:95384800-95421600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:95385800-95401800	Strong transcription	Osteobl	bone
11	chr9:95390200-95411200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:95391800-95410600	Strong transcription	Left Ventricle	heart
13	chr9:95391800-95421000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:95392000-95407200	Strong transcription	NHLF	lung
15	chr9:95392000-95414600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr9:95392000-95419600	Strong transcription	Primary T cells from cord blood	blood
17	chr9:95392200-95407600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:95392200-95410800	Strong transcription	Brain Anterior Caudate	brain
19	chr9:95392400-95420800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:95392600-95403200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:95392600-95407800	Strong transcription	Brain Germinal Matrix	brain
22	chr9:95393200-95403400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:95393200-95405600	Strong transcription	Fetal Intestine Small	intestine
24	chr9:95393200-95407600	Strong transcription	Lung	lung
25	chr9:95393200-95408400	Strong transcription	Fetal Intestine Large	intestine
26	chr9:95393200-95412000	Strong transcription	Right Ventricle	heart
27	chr9:95393200-95421200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:95393200-95421600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr9:95393600-95399600	Strong transcription	HUVEC	blood vessel
30	chr9:95393600-95405400	Strong transcription	Esophagus	oesophagus
31	chr9:95393600-95407200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:95393600-95407600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:95393600-95407600	Strong transcription	Spleen	Spleen
34	chr9:95393600-95408400	Strong transcription	Primary B cells from cord blood	blood
35	chr9:95393600-95421000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr9:95393800-95400200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:95393800-95401200	Strong transcription	Pancreas	Pancrea
38	chr9:95393800-95401200	Strong transcription	Hela-S3	cervix
39	chr9:95393800-95405600	Strong transcription	Gastric	stomach
40	chr9:95393800-95407200	Strong transcription	Brain Cingulate Gyrus	brain
41	chr9:95393800-95407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:95393800-95407600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:95393800-95408200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr9:95393800-95408400	Strong transcription	Thymus	Thymus
45	chr9:95393800-95412800	Strong transcription	Placenta	Placenta
46	chr9:95393800-95413400	Strong transcription	Dnd41	blood
47	chr9:95393800-95414000	Strong transcription	Fetal Thymus	thymus
48	chr9:95393800-95414000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr9:95393800-95414400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr9:95393800-95419200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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