Variant report

Variant	rs2387396
Chromosome Location	chr10:6360293-6360294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10795990	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10795992	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10906232	1.00[CEU][hapmap];0.94[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]
rs2021950	0.88[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs7087657	1.00[CEU][hapmap]
rs7087682	0.96[CEU][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7096921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs764189	0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7901352	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7917326	0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2387396	ITIH2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6349400-6369800	Weak transcription	Adipose Nuclei	Adipose
2	chr10:6354000-6362400	Weak transcription	Aorta	Aorta
3	chr10:6354200-6369200	Weak transcription	Brain Hippocampus Middle	brain
4	chr10:6355000-6363600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:6355800-6361200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:6356000-6388200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr10:6356200-6377600	Weak transcription	Ovary	ovary
8	chr10:6357000-6369000	Weak transcription	Brain Substantia Nigra	brain
9	chr10:6357200-6397400	Weak transcription	Pancreas	Pancrea
10	chr10:6357400-6368400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:6358600-6373600	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:6358800-6364200	Enhancers	Primary B cells from peripheral blood	blood
13	chr10:6359400-6360800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:6360000-6360400	Weak transcription	A549	lung
15	chr10:6360000-6363800	Enhancers	Primary B cells from cord blood	blood
16	chr10:6360200-6361400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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