Variant report

Variant	rs17116409
Chromosome Location	chr5:154121691-154121692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154110340..154114557-chr5:154119062..154122333,4	MCF-7	breast:
2	chr5:154121511..154123647-chr5:154211048..154213983,2	K562	blood:
3	chr5:154121676..154125151-chr5:154126453..154128268,3	MCF-7	breast:
4	chr5:154120475..154122431-chr5:154137952..154140710,2	K562	blood:
5	chr5:154086664..154088474-chr5:154121658..154123689,2	K562	blood:
6	chr5:154120886..154122562-chr5:154135110..154137055,2	K562	blood:
7	chr5:154033389..154035257-chr5:154121200..154122760,2	K562	blood:
8	chr5:154120997..154122721-chr5:154132198..154134766,2	K562	blood:
9	chr5:154121264..154124038-chr5:154128528..154131681,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1035368	1.00[TSI][hapmap]
rs12186610	0.85[EUR][1000 genomes]
rs12187572	0.85[EUR][1000 genomes]
rs12187921	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12188149	0.80[EUR][1000 genomes]
rs12188498	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12188906	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12189508	0.88[EUR][1000 genomes]
rs12300	0.90[TSI][hapmap]
rs1421813	0.80[EUR][1000 genomes]
rs1421814	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs17096232	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17116417	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17116421	1.00[TSI][hapmap]
rs17116433	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17116442	1.00[TSI][hapmap]
rs17116455	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17116489	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17116534	1.00[TSI][hapmap]
rs1974776	1.00[TSI][hapmap]
rs1974777	1.00[TSI][hapmap]
rs2258437	1.00[TSI][hapmap]
rs2396999	0.86[CHB][hapmap]
rs2544880	1.00[TSI][hapmap]
rs2644743	1.00[TSI][hapmap]
rs2644744	1.00[TSI][hapmap]
rs2688198	1.00[TSI][hapmap]
rs2688201	1.00[TSI][hapmap]
rs348739	1.00[TSI][hapmap]
rs348750	1.00[TSI][hapmap]
rs3776984	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs39614	1.00[TSI][hapmap]
rs4452598	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4626377	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56773390	0.82[EUR][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs6895741	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs702742	1.00[TSI][hapmap]
rs73806917	0.85[EUR][1000 genomes]
rs73807206	0.80[EUR][1000 genomes]
rs73807207	0.80[EUR][1000 genomes]
rs73809507	0.80[EUR][1000 genomes]
rs7709899	0.80[EUR][1000 genomes]
rs7716019	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs816717	1.00[TSI][hapmap]
rs816718	0.95[TSI][hapmap]
rs816720	1.00[TSI][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	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154107200-154133200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:154112200-154123600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:154116200-154132400	Weak transcription	Fetal Intestine Small	intestine
4	chr5:154117800-154123600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:154117800-154123600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:154117800-154128600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:154117800-154133000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:154118000-154123600	Weak transcription	HepG2	liver
9	chr5:154118000-154133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:154119600-154133400	Weak transcription	Lung	lung
11	chr5:154120000-154123600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:154120800-154122600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr5:154120800-154123200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:154121000-154123400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:154121000-154123400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:154121000-154130200	Weak transcription	Liver	Liver
17	chr5:154121000-154132800	Weak transcription	Psoas Muscle	Psoas
18	chr5:154121200-154121800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:154121200-154121800	Enhancers	Stomach Smooth Muscle	stomach
20	chr5:154121200-154123400	Weak transcription	Pancreas	Pancrea
21	chr5:154121200-154123400	Weak transcription	K562	blood
22	chr5:154121200-154123600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:154121200-154123600	Weak transcription	Right Ventricle	heart
24	chr5:154121200-154125600	Weak transcription	Brain Anterior Caudate	brain
25	chr5:154121200-154125800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:154121200-154125800	Weak transcription	Brain Substantia Nigra	brain
27	chr5:154121200-154128600	Weak transcription	Right Atrium	heart
28	chr5:154121200-154128800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:154121200-154128800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:154121200-154132600	Weak transcription	Gastric	stomach
31	chr5:154121200-154132800	Weak transcription	Brain Angular Gyrus	brain
32	chr5:154121400-154122600	Weak transcription	Placenta	Placenta
33	chr5:154121400-154123400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:154121400-154125600	Weak transcription	Adipose Nuclei	Adipose
35	chr5:154121400-154125600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:154121400-154125800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:154121400-154127800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:154121600-154123600	Weak transcription	Stomach Mucosa	stomach
39	chr5:154121600-154132600	Weak transcription	Rectal Smooth Muscle	rectum

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