Variant report

Variant	rs3168135
Chromosome Location	chr11:58386177-58386178
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	chr11:58384359-58386248	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:58385052-58397818	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:58385876..58387982-chr11:58406021..58408836,2	MCF-7	breast:
2	chr11:58384026..58388374-chr11:58388500..58391345,3	K562	blood:
3	chr11:58380066..58382513-chr11:58384585..58386505,2	K562	blood:

Variant related genes	Relation type
CNTF	TF binding region
ENSG00000242689	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10896785	0.81[AMR][1000 genomes]
rs10896787	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896788	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896794	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896795	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896796	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229463	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11229505	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229512	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229519	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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]
rs11229555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601687	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605269	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605297	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11605683	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12285111	0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12787765	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12799215	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12800710	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12808544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17567523	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1893902	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1938598	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986404	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2275993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298608	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6591475	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7102510	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7102852	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7110210	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7925560	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7927966	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8373	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3168135	MS4A10	cis	cerebellum	SCAN
rs3168135	OR4C6	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58363000-58393200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:58375800-58388200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:58376600-58388400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:58376600-58391800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:58376600-58395800	Strong transcription	Fetal Thymus	thymus
6	chr11:58376600-58396200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:58376800-58388200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr11:58376800-58391600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:58376800-58393200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr11:58376800-58395200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:58376800-58395600	Strong transcription	Dnd41	blood
12	chr11:58377000-58391400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:58377000-58391600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:58377000-58394600	Strong transcription	K562	blood
15	chr11:58377200-58387000	Strong transcription	Thymus	Thymus
16	chr11:58377200-58387200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:58377200-58388000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:58377200-58388600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:58377200-58388800	Strong transcription	HUVEC	blood vessel
20	chr11:58377200-58389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:58377200-58393000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:58377200-58393800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:58377200-58393800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:58377200-58394000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:58377200-58394000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:58377200-58394000	Strong transcription	Liver	Liver
27	chr11:58377200-58394000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr11:58377200-58394400	Strong transcription	A549	lung
29	chr11:58377200-58394600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr11:58377200-58394800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:58377200-58394800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr11:58377200-58397200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:58377400-58386800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:58377400-58387000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:58377400-58387000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr11:58377400-58387600	Strong transcription	Primary T cells from cord blood	blood
37	chr11:58377400-58387600	Strong transcription	Fetal Brain Female	brain
38	chr11:58377400-58388200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:58377400-58391200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:58377400-58393600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr11:58377400-58394600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr11:58377400-58394600	Strong transcription	Fetal Intestine Large	intestine
43	chr11:58377400-58394800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr11:58377400-58394800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr11:58377400-58395200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr11:58377600-58388400	Strong transcription	GM12878-XiMat	blood
47	chr11:58377600-58395200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr11:58377800-58388800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:58377800-58393800	Strong transcription	Primary B cells from cord blood	blood
50	chr11:58378000-58392800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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