Variant report

Variant	rs9808245
Chromosome Location	chr2:190210891-190210892
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190206539..190208625-chr2:190208807..190211103,2	K562	blood:
2	chr2:190210465..190212459-chr2:190217918..190220688,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC40A1-1	chr2:190210854-190211020	NONHSAT076051

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10174225	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177513	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497699	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10497701	0.85[CHB][hapmap]
rs10497702	0.85[CHB][hapmap]
rs10755004	0.80[CEU][hapmap]
rs1157910	0.80[CEU][hapmap]
rs11677073	0.83[ASN][1000 genomes]
rs11681937	0.83[ASN][1000 genomes]
rs11684417	0.83[ASN][1000 genomes]
rs11684869	1.00[CHB][hapmap]
rs11693810	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13010531	0.80[CEU][hapmap]
rs13032853	0.80[CEU][hapmap]
rs13406671	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464136	0.87[EUR][1000 genomes]
rs1515873	0.83[ASN][1000 genomes]
rs1519182	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1519185	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520857	0.80[CEU][hapmap]
rs1520862	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17198780	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17198787	1.00[CHB][hapmap]
rs17198857	0.85[CHB][hapmap]
rs17198892	0.85[CHB][hapmap]
rs17270952	0.86[ASN][1000 genomes]
rs17270966	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs17270973	1.00[CHB][hapmap]
rs17271015	0.83[ASN][1000 genomes]
rs17271036	0.85[CHB][hapmap]
rs17271043	0.85[CHB][hapmap]
rs17271057	0.85[CHB][hapmap]
rs1996576	0.83[ASN][1000 genomes]
rs2289225	0.85[CHB][hapmap]
rs2304701	0.85[CHB][hapmap]
rs2680629	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683013	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683014	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683015	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683016	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667281	0.80[CEU][hapmap]
rs55726777	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61528955	0.83[ASN][1000 genomes]
rs62182060	0.83[ASN][1000 genomes]
rs62182061	0.83[ASN][1000 genomes]
rs62182066	0.83[ASN][1000 genomes]
rs62182067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182068	0.83[ASN][1000 genomes]
rs62182069	0.83[ASN][1000 genomes]
rs62182420	0.81[ASN][1000 genomes]
rs62183846	0.83[ASN][1000 genomes]
rs62183848	0.83[ASN][1000 genomes]
rs6434339	0.80[CEU][hapmap]
rs72912280	0.83[ASN][1000 genomes]
rs72912286	0.83[ASN][1000 genomes]
rs72914141	0.83[ASN][1000 genomes]
rs7564429	0.83[ASN][1000 genomes]
rs7576165	0.80[CEU][hapmap]
rs7577872	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963738	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9808245	COL5A2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190204600-190211400	Weak transcription	Osteobl	bone
2	chr2:190205000-190211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:190207800-190211800	Weak transcription	NH-A	brain
4	chr2:190209800-190211400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:190210200-190211400	Weak transcription	Colon Smooth Muscle	Colon

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