Variant report

Variant	rs17116433
Chromosome Location	chr5:154169739-154169740
allele	A/G
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	chr5:154169453-154170269	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:154169674-154169919	K562	blood:	n/a	n/a
3	POLR2A	chr5:154169375-154170222	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:154169242..154171344-chr5:154172525..154174056,2	MCF-7	breast:
2	chr5:154168441..154171085-chr5:154196369..154197910,2	MCF-7	breast:

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1035368	1.00[CHB][hapmap]
rs10515727	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12186480	0.83[EUR][1000 genomes]
rs12186610	0.91[EUR][1000 genomes]
rs12187572	0.90[EUR][1000 genomes]
rs12187890	0.84[EUR][1000 genomes]
rs12187921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188149	0.86[EUR][1000 genomes]
rs12188498	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12188828	1.00[CHB][hapmap]
rs12188906	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12189508	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421813	0.86[EUR][1000 genomes]
rs1421814	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1421815	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1421819	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs17096232	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17116417	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17116421	1.00[CHB][hapmap]
rs17116442	1.00[CHB][hapmap]
rs17116455	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17116489	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17116638	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs180846	1.00[CHB][hapmap]
rs1974776	1.00[CHB][hapmap]
rs1974777	1.00[CHB][hapmap]
rs2042168	1.00[CHB][hapmap]
rs2161128	1.00[CHB][hapmap]
rs2258437	1.00[CHB][hapmap]
rs2291780	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2544860	0.86[CHB][hapmap]
rs2544880	1.00[CHB][hapmap]
rs2544884	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2644743	1.00[CHB][hapmap]
rs2688201	1.00[CHB][hapmap]
rs32427	0.86[CHB][hapmap]
rs348739	1.00[CHB][hapmap]
rs348748	1.00[CHB][hapmap]
rs348749	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs348750	1.00[CHB][hapmap]
rs348752	1.00[CHB][hapmap]
rs3776984	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs39614	1.00[CHB][hapmap]
rs4452598	0.92[EUR][1000 genomes]
rs4626377	0.92[EUR][1000 genomes]
rs55692274	0.84[EUR][1000 genomes]
rs56773390	0.87[EUR][1000 genomes]
rs56895891	0.80[EUR][1000 genomes]
rs6580123	0.84[EUR][1000 genomes]
rs6865950	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs6895741	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs702742	1.00[CHB][hapmap]
rs73806917	0.90[EUR][1000 genomes]
rs73807206	0.86[EUR][1000 genomes]
rs73807207	0.86[EUR][1000 genomes]
rs73807213	0.84[EUR][1000 genomes]
rs73809507	0.86[EUR][1000 genomes]
rs7709899	0.86[EUR][1000 genomes]
rs7716019	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs816717	1.00[CHB][hapmap]
rs816718	1.00[CHB][hapmap]
rs816720	1.00[CHB][hapmap]
rs816747	0.85[CHB][hapmap]
rs960499	0.85[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154151600-154171200	Weak transcription	Fetal Brain Male	brain
2	chr5:154161800-154169800	Weak transcription	HMEC	breast
3	chr5:154162400-154170200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:154163000-154169800	Weak transcription	Fetal Brain Female	brain
5	chr5:154163000-154171200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:154163200-154169800	Weak transcription	NHLF	lung
7	chr5:154163400-154171200	Weak transcription	HSMMtube	muscle
8	chr5:154163600-154169800	Weak transcription	Primary B cells from cord blood	blood
9	chr5:154164000-154169800	Weak transcription	Brain Germinal Matrix	brain
10	chr5:154164000-154173600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:154164200-154176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:154164600-154188200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:154165000-154171000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:154165600-154169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:154166000-154176000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:154166400-154173200	Strong transcription	Fetal Intestine Small	intestine
17	chr5:154167000-154203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:154167800-154169800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:154167800-154169800	Weak transcription	Liver	Liver
20	chr5:154167800-154171000	Weak transcription	HSMM	muscle
21	chr5:154167800-154171000	Weak transcription	NHDF-Ad	bronchial
22	chr5:154168000-154169800	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:154168000-154169800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:154168000-154171000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:154168000-154171200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:154168000-154171400	Weak transcription	Fetal Kidney	kidney
27	chr5:154168000-154171600	Weak transcription	Stomach Mucosa	stomach
28	chr5:154168000-154174600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:154168200-154169800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:154168200-154169800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:154168200-154169800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:154168200-154169800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:154168200-154169800	Weak transcription	Brain Anterior Caudate	brain
34	chr5:154168200-154169800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:154168200-154169800	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:154168200-154170000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:154168200-154170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:154168200-154170200	Weak transcription	Pancreas	Pancrea
39	chr5:154168200-154171200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:154168200-154172800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:154168200-154173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr5:154168400-154169800	Weak transcription	Brain Substantia Nigra	brain
43	chr5:154168400-154169800	Weak transcription	Right Ventricle	heart
44	chr5:154168400-154169800	Weak transcription	HUVEC	blood vessel
45	chr5:154168400-154170000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:154168400-154171400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:154168600-154169800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:154168600-154169800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:154168600-154169800	Weak transcription	Right Atrium	heart
50	chr5:154168600-154171800	Weak transcription	Fetal Heart	heart

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