Variant report

Variant	rs828877
Chromosome Location	chr2:74364848-74364849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74345218..74347575-chr2:74362895..74365930,3	MCF-7	breast:
2	chr2:74065563..74067367-chr2:74363020..74364872,2	K562	blood:
3	chr2:74347221..74348917-chr2:74363976..74366129,3	K562	blood:
4	chr2:74364840..74367040-chr2:74367594..74369690,3	MCF-7	breast:
5	chr2:74363441..74365761-chr2:74425678..74427198,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257800	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11126426	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1620482	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1667601	0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1667605	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1667606	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667609	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1723292	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35864597	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs702466	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7559252	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7562297	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs828856	0.81[ASN][1000 genomes]
rs828873	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828882	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828883	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828884	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828885	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828886	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828888	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828889	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828903	1.00[JPT][hapmap]
rs844168	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[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	nsv525117	chr2:74358901-74374641	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs828877	MTHFD2	cis	lymphoblastoid	seeQTL
rs828877	ZNF638	cis	cerebellum	SCAN
rs828877	NAT8	cis	parietal	SCAN
rs828877	LBX2	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74348200-74367600	Weak transcription	Brain Anterior Caudate	brain
2	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:74357600-74373800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:74357800-74367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:74357800-74373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:74358200-74373800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:74358600-74367800	Weak transcription	Osteobl	bone
9	chr2:74358600-74368800	Weak transcription	NHDF-Ad	bronchial
10	chr2:74358800-74373800	Weak transcription	HUVEC	blood vessel
11	chr2:74359200-74373600	Weak transcription	Fetal Heart	heart
12	chr2:74359400-74367600	Weak transcription	HSMM	muscle
13	chr2:74359400-74373600	Weak transcription	Primary B cells from cord blood	blood
14	chr2:74359600-74373400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:74359600-74373800	Weak transcription	Small Intestine	intestine
16	chr2:74359800-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:74359800-74373600	Weak transcription	NH-A	brain
18	chr2:74360000-74369800	Weak transcription	Colonic Mucosa	Colon
19	chr2:74360200-74373600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:74360400-74366600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:74360600-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:74360800-74373600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:74360800-74373800	Weak transcription	Placenta	Placenta
24	chr2:74360800-74374000	Weak transcription	HSMMtube	muscle
25	chr2:74361200-74365800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:74362000-74371600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:74362000-74373600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:74362200-74365000	Weak transcription	Ovary	ovary
29	chr2:74362200-74365200	Weak transcription	A549	lung
30	chr2:74362200-74365400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:74362200-74365400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:74362200-74366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:74362200-74366400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:74362200-74366400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:74362200-74366400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:74362200-74366600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:74362200-74366800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:74362200-74367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:74362200-74367600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:74362200-74367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:74362200-74367600	Weak transcription	Fetal Intestine Large	intestine
42	chr2:74362200-74367600	Weak transcription	Gastric	stomach
43	chr2:74362200-74367600	Weak transcription	Left Ventricle	heart
44	chr2:74362200-74367600	Weak transcription	Lung	lung
45	chr2:74362200-74367600	Weak transcription	Spleen	Spleen
46	chr2:74362200-74367800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:74362200-74368600	Weak transcription	Pancreas	Pancrea
48	chr2:74362200-74369000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:74362200-74369200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:74362200-74371400	Weak transcription	Brain Substantia Nigra	brain

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