Variant report

Variant	rs9321243
Chromosome Location	chr6:99335730-99335731
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:99295395..99298026-chr6:99333556..99335799,2	K562	blood:
2	chr6:99334583..99336582-chr6:99336803..99339769,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10484609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12110702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs13194064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200668	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195842	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2124137	0.97[ASN][1000 genomes]
rs2267924	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300063	0.83[CEU][hapmap]
rs2572095	0.83[CEU][hapmap]
rs35727107	0.86[EUR][1000 genomes]
rs3765239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407721	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67597785	0.92[ASN][1000 genomes]
rs6929427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7453242	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs760765	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760766	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742800	0.81[CEU][hapmap]
rs9372982	0.83[CEU][hapmap]
rs9375713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375721	0.83[CEU][hapmap]
rs9375728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375729	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs9375730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375750	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375807	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[ASN][1000 genomes]
rs9385541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385544	0.83[CEU][hapmap]
rs9388788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388789	1.00[ASN][1000 genomes]
rs9388809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9388815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388895	0.83[CEU][hapmap]
rs9402227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604253	chr6:98857397-99630038	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9321243	PRDM13	cis	parietal	SCAN
rs9321243	FBXL4	cis	multi-tissue	Pritchard
rs9321243	PRDM13	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:99294600-99347800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:99297000-99386000	Weak transcription	Fetal Brain Male	brain
3	chr6:99298600-99345400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:99304000-99358600	Weak transcription	Aorta	Aorta
5	chr6:99304600-99387200	Weak transcription	A549	lung
6	chr6:99309600-99346800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:99309600-99351600	Weak transcription	NHDF-Ad	bronchial
8	chr6:99309600-99383400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:99309800-99377400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:99311400-99356600	Weak transcription	Brain Angular Gyrus	brain
11	chr6:99312000-99370800	Weak transcription	Esophagus	oesophagus
12	chr6:99312600-99372600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:99312800-99340400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:99312800-99340800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:99312800-99351600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:99314800-99339600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:99315600-99358600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:99316800-99345400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:99318000-99346800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:99318600-99347200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:99318600-99347200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:99318600-99355800	Weak transcription	Colonic Mucosa	Colon
23	chr6:99318800-99346400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:99319200-99346800	Weak transcription	Psoas Muscle	Psoas
25	chr6:99319400-99360000	Weak transcription	NH-A	brain
26	chr6:99319400-99393600	Weak transcription	NHLF	lung
27	chr6:99319600-99345400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:99320200-99340400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:99320200-99379400	Weak transcription	NHEK	skin
30	chr6:99320400-99393600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:99320800-99340600	Weak transcription	Fetal Kidney	kidney
32	chr6:99321000-99355800	Weak transcription	Spleen	Spleen
33	chr6:99321000-99369000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:99321200-99345400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:99321400-99345600	Weak transcription	Lung	lung
36	chr6:99321400-99346600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:99321600-99359800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:99322200-99345400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:99322400-99373200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:99323200-99346200	Weak transcription	HMEC	breast
41	chr6:99323600-99349000	Weak transcription	Pancreas	Pancrea
42	chr6:99323600-99354600	Weak transcription	Brain Anterior Caudate	brain
43	chr6:99323800-99345600	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:99323800-99345800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:99324800-99345400	Weak transcription	HSMM	muscle
46	chr6:99325800-99345000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:99326000-99380600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:99326600-99346600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:99327400-99344000	Weak transcription	Placenta	Placenta
50	chr6:99328400-99339200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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