Variant report

Variant	rs17024708
Chromosome Location	chr4:149340536-149340537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10033040	1.00[JPT][hapmap]
rs10034789	0.81[CHB][hapmap]
rs10519959	0.83[CHB][hapmap]
rs12711259	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs13137647	0.94[EUR][1000 genomes]
rs1512343	0.83[CHB][hapmap]
rs1546044	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs17484601	0.83[CHB][hapmap]
rs17484671	0.83[CHB][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs17581815	0.83[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs17581975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2137338	0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2358392	0.88[EUR][1000 genomes]
rs2358393	0.87[EUR][1000 genomes]
rs2884444	0.83[EUR][1000 genomes]
rs34818230	0.87[EUR][1000 genomes]
rs4293768	0.88[EUR][1000 genomes]
rs4513547	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs4835136	0.81[CHB][hapmap]
rs61756942	0.83[EUR][1000 genomes]
rs61756945	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61763774	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61764776	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61764785	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6849903	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6850820	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs72729957	0.88[EUR][1000 genomes]
rs72729960	0.88[EUR][1000 genomes]
rs72729961	0.88[EUR][1000 genomes]
rs72729962	0.88[EUR][1000 genomes]
rs72729966	0.88[EUR][1000 genomes]
rs72729971	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72729972	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72729980	0.82[EUR][1000 genomes]
rs72729984	0.81[EUR][1000 genomes]
rs72729985	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72732326	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73855952	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7691663	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7698302	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7700126	0.83[CHB][hapmap]
rs907618	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs907620	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9307847	0.95[EUR][1000 genomes]
rs9995951	0.95[EUR][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
rs17024708	LSM6	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr4:149318800-149346600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:149320400-149351800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:149327000-149351000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:149327200-149341200	Weak transcription	Psoas Muscle	Psoas
6	chr4:149327200-149341800	Weak transcription	Right Atrium	heart
7	chr4:149327400-149346600	Weak transcription	Small Intestine	intestine
8	chr4:149327800-149346400	Weak transcription	Gastric	stomach
9	chr4:149327800-149346400	Weak transcription	Pancreas	Pancrea
10	chr4:149329600-149343800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:149334000-149341800	Weak transcription	Left Ventricle	heart
12	chr4:149335400-149346400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:149335400-149349200	Weak transcription	Fetal Heart	heart
14	chr4:149337600-149343800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:149338600-149354800	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:149339000-149340800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr4:149339000-149341400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr4:149339200-149340600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:149339400-149342200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr4:149339400-149344000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:149339800-149340800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:149340200-149356800	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:149340400-149341800	Weak transcription	Stomach Mucosa	stomach

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