Variant report

Variant	rs4670940
Chromosome Location	chr2:39714650-39714651
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39701139..39703920-chr2:39713857..39716222,2	MCF-7	breast:
2	chr2:39713314..39715657-chr2:39717549..39719178,2	K562	blood:
3	chr2:39714157..39716923-chr2:39717549..39720547,2	K562	blood:
4	chr2:39663353..39665956-chr2:39712350..39718160,5	MCF-7	breast:
5	chr2:39682594..39684277-chr2:39713260..39716183,2	MCF-7	breast:
6	chr2:39709054..39711333-chr2:39713452..39715456,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11884949	0.80[ASN][1000 genomes]
rs11896389	0.80[ASN][1000 genomes]
rs13420425	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17023696	0.82[JPT][hapmap]
rs17531732	1.00[ASN][1000 genomes]
rs2111383	0.82[JPT][hapmap]
rs2287088	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55761128	0.80[ASN][1000 genomes]
rs58177306	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59109595	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924009	0.80[ASN][1000 genomes]
rs7577097	0.89[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4670940	SOS1	cis	cerebellum	SCAN
rs4670940	SLC8A1	cis	parietal	SCAN
rs4670940	HEATR5B	cis	parietal	SCAN
rs4670940	MAP4K3	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39697400-39715400	Weak transcription	Pancreas	Pancrea
2	chr2:39697400-39722000	Weak transcription	Fetal Stomach	stomach
3	chr2:39697400-39722000	Weak transcription	Right Ventricle	heart
4	chr2:39697400-39724200	Weak transcription	Gastric	stomach
5	chr2:39702200-39726000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:39705400-39719400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:39705600-39715200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:39705600-39719000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:39705600-39721600	Weak transcription	Psoas Muscle	Psoas
10	chr2:39706200-39715400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:39707400-39724200	Weak transcription	Fetal Brain Male	brain
12	chr2:39708200-39715400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:39710200-39715200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:39710600-39716400	Enhancers	A549	lung
15	chr2:39710800-39717800	Weak transcription	Primary B cells from cord blood	blood
16	chr2:39711400-39714800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:39711400-39717400	Weak transcription	Stomach Mucosa	stomach
18	chr2:39711400-39718800	Weak transcription	K562	blood
19	chr2:39711600-39715000	Weak transcription	Fetal Lung	lung
20	chr2:39711600-39715200	Weak transcription	Ovary	ovary
21	chr2:39711600-39721800	Weak transcription	Left Ventricle	heart
22	chr2:39711600-39722000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39711600-39722000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:39712000-39715400	Weak transcription	Right Atrium	heart
25	chr2:39712400-39719200	Weak transcription	Fetal Heart	heart
26	chr2:39712400-39748600	Weak transcription	Aorta	Aorta
27	chr2:39712600-39714800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:39712600-39716000	Enhancers	HSMM	muscle
29	chr2:39713200-39716000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:39713200-39716000	Enhancers	HSMMtube	muscle
31	chr2:39713200-39716400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:39713600-39715000	Weak transcription	NHLF	lung
33	chr2:39713600-39716600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:39713600-39722000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:39713800-39714800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:39713800-39714800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:39713800-39715000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:39713800-39715000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:39713800-39715000	Weak transcription	NHDF-Ad	bronchial
40	chr2:39713800-39715400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:39713800-39715400	Weak transcription	Placenta	Placenta
42	chr2:39713800-39721600	Weak transcription	Lung	lung
43	chr2:39714000-39715000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:39714200-39715200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr2:39714400-39714800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:39714400-39715000	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:39714400-39715200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:39714400-39715200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:39714400-39715600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:39714400-39715600	Enhancers	HUES64 Cell Line	embryonic stem cell

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