Variant report

Variant	rs828903
Chromosome Location	chr2:74436721-74436722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74435328..74437744-chr2:74484533..74487667,3	MCF-7	breast:
2	chr2:74435694..74437496-chr2:74451439..74453723,2	MCF-7	breast:
3	chr2:74431773..74434450-chr2:74434840..74436858,2	MCF-7	breast:
4	chr2:74434810..74438446-chr2:74445370..74448587,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1095968	0.81[EUR][1000 genomes]
rs11126426	0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12196	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13426653	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1620482	0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1667601	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1667609	0.86[ASN][1000 genomes]
rs1723281	0.81[EUR][1000 genomes]
rs1723285	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs3108164	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs35864597	0.80[ASN][1000 genomes]
rs4853016	0.82[EUR][1000 genomes]
rs6546893	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546894	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs702462	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7340453	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7559252	0.87[ASN][1000 genomes]
rs8001	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828853	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828856	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828857	0.82[EUR][1000 genomes]
rs828858	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs828877	1.00[JPT][hapmap]
rs828882	0.81[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs828883	0.81[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs828884	0.81[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs828888	0.81[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs828889	0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs844168	0.83[CEU][hapmap];1.00[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs828903	TGFA	cis	parietal	SCAN
rs828903	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427200-74438200	Weak transcription	Fetal Kidney	kidney
2	chr2:74427400-74441000	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:74427400-74441200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:74427400-74448400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:74427400-74453000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:74427400-74453200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:74427400-74460200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
9	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
10	chr2:74427600-74442600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
12	chr2:74428000-74448600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:74428600-74449600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:74429000-74450600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:74429000-74453200	Weak transcription	Ovary	ovary
16	chr2:74429200-74452800	Weak transcription	Fetal Heart	heart
17	chr2:74432200-74441600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr2:74432600-74444600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr2:74432800-74441800	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:74433600-74441800	Strong transcription	Fetal Stomach	stomach
21	chr2:74433600-74443000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:74433600-74444200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:74433600-74447200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:74433600-74447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:74433600-74447600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:74433600-74447600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:74433600-74448400	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:74433800-74437800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:74433800-74439400	Weak transcription	Aorta	Aorta
30	chr2:74433800-74439600	Weak transcription	Fetal Intestine Small	intestine
31	chr2:74433800-74447400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr2:74433800-74447400	Strong transcription	Dnd41	blood
33	chr2:74433800-74447600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:74433800-74447600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:74433800-74448400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:74433800-74449200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:74433800-74449200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:74433800-74449400	Strong transcription	NHEK	skin
39	chr2:74433800-74449600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:74433800-74449800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:74433800-74461800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:74434000-74436800	Weak transcription	Small Intestine	intestine
43	chr2:74434000-74438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:74434000-74438400	Weak transcription	Pancreas	Pancrea
45	chr2:74434000-74444800	Strong transcription	Hela-S3	cervix
46	chr2:74434000-74453000	Weak transcription	Psoas Muscle	Psoas
47	chr2:74434200-74436800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:74434200-74436800	Weak transcription	Colonic Mucosa	Colon
49	chr2:74434200-74438000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:74434200-74439000	Strong transcription	Muscle Satellite Cultured Cells	--

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