Variant report

Variant	rs10187034
Chromosome Location	chr2:111812617-111812618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111811305..111813618-chr2:111877907..111879884,2	MCF-7	breast:
2	chr2:111811276..111814193-chr2:111817027..111819941,2	K562	blood:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11123325	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13000374	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1821969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898846	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2880119	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848374	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4849360	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759108	0.86[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10187034	JHDM1D	trans	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:111806600-111813400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:111808400-111812800	Weak transcription	Thymus	Thymus
4	chr2:111808600-111812800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:111810200-111816800	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:111810400-111812800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr2:111811000-111813000	Enhancers	GM12878-XiMat	blood
8	chr2:111811400-111813400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:111811400-111813600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:111811600-111813200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:111811600-111813200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:111811600-111813400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:111811600-111813600	Enhancers	Fetal Thymus	thymus
14	chr2:111811600-111815200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:111811800-111813800	Weak transcription	Right Atrium	heart
16	chr2:111811800-111816600	Enhancers	Primary B cells from cord blood	blood
17	chr2:111812000-111813400	Enhancers	Primary T cells from cord blood	blood
18	chr2:111812200-111813200	Weak transcription	Fetal Heart	heart
19	chr2:111812200-111813400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr2:111812400-111813200	Enhancers	Fetal Kidney	kidney
21	chr2:111812600-111812800	Bivalent Enhancer	NH-A	brain
22	chr2:111812600-111813000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:111812600-111813200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:111812600-111813200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:111812600-111813200	Enhancers	Colonic Mucosa	Colon
26	chr2:111812600-111813200	Enhancers	Pancreas	Pancrea
27	chr2:111812600-111813400	Enhancers	Spleen	Spleen

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