Variant report

Variant	rs9307847
Chromosome Location	chr4:149327521-149327522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12711259	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13109808	0.94[JPT][hapmap]
rs13109933	0.94[JPT][hapmap]
rs13112423	0.94[JPT][hapmap]
rs13137647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512327	0.94[JPT][hapmap]
rs1546044	0.82[CEU][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17024708	1.00[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs17484671	0.83[EUR][1000 genomes]
rs17581815	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs17581975	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1913023	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2137331	0.94[JPT][hapmap]
rs2137338	0.86[CHB][hapmap]
rs2358392	0.87[EUR][1000 genomes]
rs2358393	0.87[EUR][1000 genomes]
rs2884444	0.82[EUR][1000 genomes]
rs34818230	0.86[EUR][1000 genomes]
rs4293768	0.87[EUR][1000 genomes]
rs4513547	0.87[EUR][1000 genomes]
rs61756942	0.82[EUR][1000 genomes]
rs61756945	0.96[EUR][1000 genomes]
rs61763774	0.95[EUR][1000 genomes]
rs61764776	0.96[EUR][1000 genomes]
rs61764785	0.96[EUR][1000 genomes]
rs6831212	0.94[JPT][hapmap]
rs6849903	0.94[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs6850820	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72729957	0.87[EUR][1000 genomes]
rs72729960	0.87[EUR][1000 genomes]
rs72729961	0.87[EUR][1000 genomes]
rs72729962	0.87[EUR][1000 genomes]
rs72729966	0.87[EUR][1000 genomes]
rs72729971	0.87[EUR][1000 genomes]
rs72729972	0.92[EUR][1000 genomes]
rs72729980	0.82[EUR][1000 genomes]
rs72729984	0.80[EUR][1000 genomes]
rs72729985	0.96[EUR][1000 genomes]
rs72732326	0.92[EUR][1000 genomes]
rs73855952	0.92[EUR][1000 genomes]
rs7698302	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs907618	0.94[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs907620	0.81[EUR][1000 genomes]
rs9995951	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016966	chr4:149209467-149341037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv530433	chr4:149277637-149669181	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9307847	LSM6	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149297800-149350000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:149299000-149329000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:149307600-149336600	Weak transcription	Aorta	Aorta
4	chr4:149312800-149338800	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:149318800-149346600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:149319000-149339000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:149319200-149335000	Weak transcription	Esophagus	oesophagus
8	chr4:149319200-149339200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:149319400-149334600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:149320400-149351800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:149321400-149328000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:149325600-149328400	Enhancers	Liver	Liver
13	chr4:149325800-149338600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:149326400-149327800	Enhancers	Duodenum Mucosa	Duodenum
15	chr4:149326400-149327800	Enhancers	Pancreas	Pancrea
16	chr4:149326800-149334600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:149327000-149328000	Weak transcription	Stomach Mucosa	stomach
18	chr4:149327000-149351000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:149327200-149327600	Weak transcription	Gastric	stomach
20	chr4:149327200-149327800	Enhancers	Fetal Stomach	stomach
21	chr4:149327200-149332800	Weak transcription	Right Ventricle	heart
22	chr4:149327200-149333200	Weak transcription	Ovary	ovary
23	chr4:149327200-149341200	Weak transcription	Psoas Muscle	Psoas
24	chr4:149327200-149341800	Weak transcription	Right Atrium	heart
25	chr4:149327400-149333200	Weak transcription	Left Ventricle	heart
26	chr4:149327400-149346600	Weak transcription	Small Intestine	intestine

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