Variant report

Variant	rs4952447
Chromosome Location	chr2:40334899-40334900
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	chr2:40334175..40336560-chr2:40339727..40341466,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17025097	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs3922283	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs6736628	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv275350	chr2:40332851-40338067	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4952447	EIF2AK2	cis	parietal	SCAN
rs4952447	SOS1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40321200-40354600	Weak transcription	Right Ventricle	heart
2	chr2:40322800-40350200	Weak transcription	Fetal Brain Male	brain
3	chr2:40328000-40365600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:40329000-40341400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:40329600-40341400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:40329800-40337400	Weak transcription	Left Ventricle	heart
7	chr2:40329800-40342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:40329800-40345200	Weak transcription	Fetal Thymus	thymus
9	chr2:40331000-40340800	Weak transcription	Dnd41	blood
10	chr2:40331200-40350200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:40331200-40351200	Weak transcription	Fetal Stomach	stomach
12	chr2:40333000-40351000	Weak transcription	Aorta	Aorta
13	chr2:40333200-40342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:40333400-40339000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:40333400-40340800	Weak transcription	Psoas Muscle	Psoas
16	chr2:40333400-40354400	Weak transcription	NH-A	brain
17	chr2:40333600-40336400	Weak transcription	Fetal Heart	heart
18	chr2:40333600-40336400	Weak transcription	HSMM	muscle
19	chr2:40333600-40339000	Weak transcription	NHDF-Ad	bronchial
20	chr2:40333600-40340600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:40333800-40340200	Weak transcription	Osteobl	bone
22	chr2:40334000-40335000	Enhancers	Ovary	ovary
23	chr2:40334400-40336000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:40334600-40354800	Weak transcription	Fetal Brain Female	brain

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