Variant report

Variant	rs5548
Chromosome Location	chr2:40340696-40340697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr2:40340117-40340938	SK-N-SH	brain:	n/a	n/a
2	EP300	chr2:40340451-40340870	SK-N-SH_RA	brain:	n/a	n/a
3	TEAD4	chr2:40340191-40341029	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr2:40340109-40341127	SK-N-SH	brain:	n/a	n/a
5	JUND	chr2:40340124-40341045	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:40340004-40341144	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr2:40340198-40340960	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr2:40340044-40341069	SK-N-SH	brain:	n/a	n/a
9	TEAD4	chr2:40340242-40340880	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr2:40340237-40340887	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:40340013-40341122	SK-N-SH	brain:	n/a	n/a
12	GATA2	chr2:40340612-40340992	SH-SY5Y	brain:	n/a	n/a
13	PBX3	chr2:40340053-40341050	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr2:40340066-40341011	SK-N-SH	brain:	n/a	n/a
15	EP300	chr2:40340159-40341061	SK-N-SH	brain:	n/a	n/a
16	EP300	chr2:40340546-40340870	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40334175..40336560-chr2:40339727..40341466,2	MCF-7	breast:

Variant related genes	Relation type
SLC8A1-AS1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13001035	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13002111	0.82[CEU][hapmap]
rs13020366	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35424315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs381171	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5555	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

No data

Chromatin state (count:34 , 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	chr2:40329800-40342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:40329800-40345200	Weak transcription	Fetal Thymus	thymus
8	chr2:40331000-40340800	Weak transcription	Dnd41	blood
9	chr2:40331200-40350200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:40331200-40351200	Weak transcription	Fetal Stomach	stomach
11	chr2:40333000-40351000	Weak transcription	Aorta	Aorta
12	chr2:40333200-40342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:40333400-40340800	Weak transcription	Psoas Muscle	Psoas
14	chr2:40333400-40354400	Weak transcription	NH-A	brain
15	chr2:40334600-40354800	Weak transcription	Fetal Brain Female	brain
16	chr2:40336600-40345600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:40338200-40341400	Weak transcription	Left Ventricle	heart
18	chr2:40339000-40342600	Enhancers	NHDF-Ad	bronchial
19	chr2:40339000-40345800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:40339800-40341000	Weak transcription	Fetal Heart	heart
21	chr2:40339800-40341400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:40340000-40342000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:40340000-40342400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:40340200-40340800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:40340200-40340800	Enhancers	HMEC	breast
26	chr2:40340200-40341000	Enhancers	HSMM	muscle
27	chr2:40340200-40341200	Enhancers	Osteobl	bone
28	chr2:40340200-40341600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:40340200-40345200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:40340200-40345600	Weak transcription	Small Intestine	intestine
31	chr2:40340400-40340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:40340400-40340800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:40340600-40341000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:40340600-40351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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