Variant report

Variant	rs25941
Chromosome Location	chr5:14680451-14680452
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	POLR2A	chr5:14680436-14680981	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14663911..14666053-chr5:14679468..14682192,2	MCF-7	breast:
2	chr5:14663431..14670152-chr5:14672054..14680588,17	K562	blood:

Variant related genes	Relation type
FAM105B	TF binding region
ENSG00000154124	Chromatin interaction
ENSG00000261360	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13159680	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149389	1.00[CEU][hapmap]
rs149497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs152719	0.94[ASN][1000 genomes]
rs152970	0.94[ASN][1000 genomes]
rs152971	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs152972	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs152973	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153827	1.00[CEU][hapmap]
rs153828	1.00[CEU][hapmap]
rs153831	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153832	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153833	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153835	0.94[ASN][1000 genomes]
rs153836	0.84[EUR][1000 genomes]
rs153837	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153934	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154667	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249895	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2011206	0.85[EUR][1000 genomes]
rs2455240	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs250878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs25942	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs25943	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs28107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31993	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs31994	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs31995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34087737	0.82[ASN][1000 genomes]
rs34617159	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs430035	0.91[EUR][1000 genomes]
rs455943	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs456977	0.94[EUR][1000 genomes]
rs457377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs458863	0.91[EUR][1000 genomes]
rs461015	0.91[EUR][1000 genomes]
rs461056	0.94[EUR][1000 genomes]
rs461154	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs620434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1801565	chr5:14671030-14684471	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14666400-14681600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:14666400-14688200	Weak transcription	Ovary	ovary
3	chr5:14666600-14688200	Weak transcription	Brain Germinal Matrix	brain
4	chr5:14667000-14681200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:14667000-14690400	Weak transcription	Fetal Brain Male	brain
6	chr5:14672000-14684200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:14672200-14690400	Strong transcription	Hela-S3	cervix
8	chr5:14673000-14681400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:14673200-14681400	Weak transcription	Brain Angular Gyrus	brain
10	chr5:14673800-14690000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:14674000-14712800	Strong transcription	Fetal Intestine Large	intestine
12	chr5:14674600-14681400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:14674600-14687200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:14674600-14688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:14674600-14695600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:14675200-14695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:14675600-14682200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:14675800-14680600	Enhancers	Fetal Heart	heart
19	chr5:14675800-14685400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:14676000-14682000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:14676200-14681600	Weak transcription	Brain Substantia Nigra	brain
22	chr5:14676600-14681400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:14676800-14680600	Weak transcription	Colonic Mucosa	Colon
24	chr5:14676800-14681200	Weak transcription	Fetal Lung	lung
25	chr5:14676800-14681400	Weak transcription	Small Intestine	intestine
26	chr5:14676800-14683600	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:14676800-14687800	Weak transcription	Fetal Kidney	kidney
28	chr5:14676800-14690600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:14676800-14705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:14677000-14681200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr5:14677000-14681400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:14677000-14681600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:14677000-14682200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:14677000-14685800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:14677000-14688400	Weak transcription	Stomach Mucosa	stomach
36	chr5:14677000-14695200	Strong transcription	K562	blood
37	chr5:14677600-14689800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:14677600-14705600	Strong transcription	Dnd41	blood
39	chr5:14677800-14685600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:14677800-14685800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr5:14677800-14704000	Strong transcription	HepG2	liver
42	chr5:14678000-14680800	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr5:14678000-14683200	Strong transcription	Liver	Liver
44	chr5:14678000-14685200	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:14678000-14686000	Strong transcription	Primary T cells from cord blood	blood
46	chr5:14678000-14689800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr5:14678000-14690200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr5:14678000-14690200	Strong transcription	Primary B cells from cord blood	blood
49	chr5:14678200-14681600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:14678200-14681600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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