Variant report

Variant	rs828860
Chromosome Location	chr2:74411281-74411282
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	chr2:74410706..74412513-chr2:74413665..74416302,2	K562	blood:
2	chr2:74405414..74407856-chr2:74411125..74415681,6	K562	blood:

Variant related genes	Relation type
ENSG00000114978	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1056528	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095966	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1095967	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12469365	0.86[EUR][1000 genomes]
rs1667600	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1667610	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1667627	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108163	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108165	0.86[EUR][1000 genomes]
rs4630794	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs702465	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828852	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828861	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828874	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs828875	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828887	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828891	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828893	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844169	0.90[EUR][1000 genomes]
rs860455	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs828860	DQX1	cis	parietal	SCAN
rs828860	MTHFD2	cis	lymphoblastoid	seeQTL
rs828860	MOBK1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74406600-74412400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:74406600-74412600	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:74406600-74414800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:74407200-74415200	Weak transcription	Placenta	Placenta
5	chr2:74409200-74412200	Enhancers	GM12878-XiMat	blood
6	chr2:74409200-74414400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:74409200-74414600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:74409200-74414600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:74409200-74414600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:74409200-74414600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:74409200-74414600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:74409200-74419800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:74409600-74412600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:74409600-74413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:74409600-74413400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:74409600-74414600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:74409600-74415400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:74409800-74411800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:74409800-74412400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:74409800-74413200	Weak transcription	Fetal Thymus	thymus
21	chr2:74411000-74411600	Enhancers	K562	blood
22	chr2:74411000-74415000	Enhancers	Primary B cells from cord blood	blood
23	chr2:74411200-74411400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:74411200-74411600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:74411200-74412400	Enhancers	Primary neutrophils fromperipheralblood	blood

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