Variant report

No.	Distal block	Cell Line	Cell type
1	chr2:100877002..100888885-chr2:100934823..100940762,23	MCF-7	breast:
2	chr2:100878634..100879528-chr2:101043813..101044750,3	K562	blood:
3	chr2:100878643..100880888-chr2:100907492..100909514,2	K562	blood:
4	chr2:100878753..100879520-chr2:101043832..101044773,2	MCF-7	breast:
5	chr2:100877863..100879986-chr2:100936694..100939073,4	MCF-7	breast:
6	chr2:100876613..100880348-chr2:101031611..101035939,8	K562	blood:
7	chr2:100878525..100880685-chr2:100881157..100883249,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction
ENSG00000115526	Chromatin interaction

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10174820	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs10176062	0.82[JPT][hapmap]
rs10195018	0.81[JPT][hapmap]
rs11890655	0.82[JPT][hapmap]
rs11902303	0.82[JPT][hapmap]
rs12615454	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13391517	0.82[JPT][hapmap]
rs13409545	0.82[JPT][hapmap]
rs17023901	0.81[JPT][hapmap]
rs2871340	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs34529583	0.89[ASN][1000 genomes]
rs3748928	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4322861	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4438499	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4455176	0.89[ASN][1000 genomes]
rs4850925	0.82[JPT][hapmap]
rs4851278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542925	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6723909	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7556910	0.82[JPT][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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6542922	C2orf29	cis	parietal	SCAN
rs6542922	ITPRIPL1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100864200-100879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100865800-100879800	Weak transcription	Right Atrium	heart
3	chr2:100874600-100879200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:100874600-100891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:100875200-100881600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:100877000-100879200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:100877000-100879400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:100877200-100879200	Weak transcription	Fetal Lung	lung
9	chr2:100877400-100879200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:100877600-100879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:100877600-100879200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:100877600-100879800	Weak transcription	Fetal Brain Male	brain
13	chr2:100877600-100888600	Weak transcription	Ovary	ovary
14	chr2:100877800-100879200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:100877800-100879200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:100877800-100880400	Weak transcription	Placenta	Placenta
17	chr2:100878000-100879000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr2:100878000-100879400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr2:100878600-100879200	Weak transcription	Spleen	Spleen

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