Variant report

Variant	rs1108304
Chromosome Location	chr6:5785789-5785790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1108303	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12528811	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13437141	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17141291	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1815271	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2326673	0.85[GIH][hapmap];0.80[TSI][hapmap]
rs4291133	0.85[JPT][hapmap]
rs4960132	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4960134	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4960135	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4960136	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4960137	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4960138	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55864325	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55991338	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56061157	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60232193	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60475061	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60532879	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60625891	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6597163	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6917712	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6919521	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72821941	0.91[EUR][1000 genomes]
rs7760017	0.85[GIH][hapmap];0.85[TSI][hapmap]
rs7766672	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9504503	0.81[ASW][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9504505	0.83[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]

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	nsv518398	chr6:5777546-5787400	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv970669	chr6:5783028-5791204	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1108304	SSR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5753000-5786000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:5772800-5786800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:5774400-5787400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:5776400-5786800	Weak transcription	Thymus	Thymus
5	chr6:5779200-5787200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:5779600-5786600	Weak transcription	Primary T cells from cord blood	blood
7	chr6:5781600-5788000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:5781800-5786800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:5782200-5788200	Enhancers	Fetal Thymus	thymus
10	chr6:5782600-5787600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:5783600-5786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:5783600-5786800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:5783600-5787400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:5783800-5785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:5783800-5786400	Weak transcription	Brain Germinal Matrix	brain
16	chr6:5783800-5787000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:5783800-5787000	Weak transcription	Left Ventricle	heart
18	chr6:5783800-5794600	Weak transcription	Psoas Muscle	Psoas
19	chr6:5784200-5785800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:5784200-5786800	Weak transcription	Fetal Brain Male	brain
21	chr6:5784200-5787600	Weak transcription	Fetal Intestine Small	intestine
22	chr6:5784400-5787000	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:5785000-5786000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:5785000-5786000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:5785600-5786800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:5785600-5786800	Weak transcription	Fetal Muscle Trunk	muscle

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