Variant report

Variant	rs634294
Chromosome Location	chr1:85402997-85402998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11161488	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161490	0.96[EUR][1000 genomes]
rs12119401	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12124212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12125761	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028303	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs34793286	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677911	0.87[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs634294	SSX2IP	cis	parietal	SCAN
rs634294	CLCA4	cis	cerebellum	SCAN
rs634294	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs634294	MCOLN2	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85385600-85403200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:85389400-85405600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:85391800-85405800	Weak transcription	Small Intestine	intestine
4	chr1:85395400-85405800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:85396400-85410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:85396600-85410800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:85396800-85404600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:85399000-85410000	Strong transcription	GM12878-XiMat	blood
9	chr1:85400600-85404800	Weak transcription	NHLF	lung
10	chr1:85400800-85410800	Weak transcription	Fetal Lung	lung
11	chr1:85402000-85410400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:85402000-85419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:85402200-85410200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:85402200-85410400	Weak transcription	Primary T killer naive cells 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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