Variant report

Variant	rs9400287
Chromosome Location	chr6:109813344-109813345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109804488..109806145-chr6:109811754..109813384,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10080533	0.83[AFR][1000 genomes]
rs1046943	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs1054607	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1303981	0.83[AFR][1000 genomes]
rs13201430	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1322815	0.84[GIH][hapmap]
rs1406955	0.82[CEU][hapmap]
rs1476387	0.85[YRI][hapmap]
rs17070591	0.90[YRI][hapmap]
rs17070656	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs2076929	0.94[YRI][hapmap]
rs2236084	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs2277113	0.90[YRI][hapmap]
rs35146243	0.83[ASN][1000 genomes]
rs3734652	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs3757235	0.85[YRI][hapmap]
rs3778478	0.83[ASN][1000 genomes]
rs3799842	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs60640103	0.87[AFR][1000 genomes]
rs6568587	0.95[YRI][hapmap]
rs6906216	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6917383	0.95[YRI][hapmap]
rs6917713	0.83[AFR][1000 genomes]
rs6920372	0.85[YRI][hapmap]
rs6920712	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925005	0.92[ASW][hapmap];0.82[LWK][hapmap];0.95[YRI][hapmap]
rs6926096	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6927075	0.81[AFR][1000 genomes]
rs6939548	0.83[ASN][1000 genomes]
rs730089	0.85[YRI][hapmap]
rs7356790	0.92[ASW][hapmap];0.82[LWK][hapmap];0.95[YRI][hapmap]
rs736830	0.85[YRI][hapmap]
rs7757895	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs7765916	0.95[YRI][hapmap]
rs7767805	0.85[ASW][hapmap]
rs7768577	0.83[AFR][1000 genomes]
rs910730	0.85[YRI][hapmap]
rs9320289	0.87[AFR][1000 genomes]
rs9320292	0.87[AFR][1000 genomes]
rs9372223	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9374111	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9384712	0.83[CEU][hapmap]
rs9384719	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9386810	0.83[AFR][1000 genomes]
rs9386817	0.81[AFR][1000 genomes]
rs9386822	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9386828	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9386829	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9398205	0.82[AFR][1000 genomes]
rs9398210	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs9400284	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9400285	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9480947	0.85[YRI][hapmap]
rs9480956	0.94[YRI][hapmap]
rs9480969	0.83[AFR][1000 genomes]
rs9487103	0.86[YRI][hapmap]
rs9791241	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9400287	RFPL4B	cis	parietal	SCAN
rs9400287	GTF3C6	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109804400-109814200	Weak transcription	Gastric	stomach
2	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:109811400-109813600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr6:109811600-109813400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:109811600-109813400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:109811600-109813400	Enhancers	Primary T cells from cord blood	blood
7	chr6:109811600-109813600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:109811600-109813600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:109811600-109813600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:109811600-109813600	Enhancers	Fetal Thymus	thymus
11	chr6:109811600-109815000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:109811800-109813400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:109811800-109813400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:109811800-109813400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:109811800-109813600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:109812000-109813400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr6:109812000-109813400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:109812000-109813400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:109812000-109813400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:109812000-109813400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:109812000-109813400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:109812000-109813400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:109812000-109813400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:109812000-109813400	Enhancers	Thymus	Thymus
25	chr6:109812000-109813400	Flanking Active TSS	Dnd41	blood
26	chr6:109812000-109813400	Enhancers	K562	blood
27	chr6:109812000-109813600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:109812000-109813600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:109812000-109813600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:109812000-109816800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr6:109812200-109813400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:109812200-109813400	Enhancers	Primary B cells from cord blood	blood
33	chr6:109812200-109813400	Enhancers	Primary hematopoietic stem cells	blood
34	chr6:109812200-109813400	Enhancers	Fetal Muscle Leg	muscle
35	chr6:109812400-109813400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:109812400-109813400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr6:109812400-109813400	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr6:109812400-109813400	Enhancers	HSMM	muscle
39	chr6:109812400-109813400	Enhancers	HSMMtube	muscle
40	chr6:109812600-109813600	Enhancers	Brain Anterior Caudate	brain
41	chr6:109812600-109814600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:109812800-109813400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:109812800-109813400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:109812800-109813400	Enhancers	Placenta	Placenta
45	chr6:109812800-109816800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr6:109812800-109819000	Weak transcription	Fetal Kidney	kidney
47	chr6:109813000-109813400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:109813000-109814600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:109813200-109813400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:109813200-109813400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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