Variant report

Variant	rs17096232
Chromosome Location	chr5:154224949-154224950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154224707..154230790-chr5:154235604..154239293,10	K562	blood:
2	chr5:154137877..154139979-chr5:154223259..154226183,2	MCF-7	breast:
3	chr5:154213001..154215628-chr5:154222794..154224963,2	K562	blood:
4	chr5:154213002..154215551-chr5:154220667..154225908,5	MCF-7	breast:
5	chr5:154219543..154221340-chr5:154223017..154225334,2	MCF-7	breast:
6	chr5:154222966..154228276-chr5:154234542..154239768,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1035368	1.00[TSI][hapmap]
rs10515727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186480	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186610	0.85[EUR][1000 genomes]
rs12187572	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187890	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12187921	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12187934	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12187974	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12188149	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12188498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189508	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12300	0.90[TSI][hapmap]
rs1421813	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421819	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17116417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116421	1.00[TSI][hapmap]
rs17116433	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17116442	1.00[TSI][hapmap]
rs17116455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116534	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116669	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17116707	1.00[JPT][hapmap]
rs1974776	1.00[TSI][hapmap]
rs1974777	1.00[TSI][hapmap]
rs2047305	1.00[JPT][hapmap]
rs2112223	1.00[CHB][hapmap]
rs2258437	1.00[TSI][hapmap]
rs2291780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2544880	1.00[TSI][hapmap]
rs2544884	1.00[TSI][hapmap]
rs2644743	1.00[TSI][hapmap]
rs2644744	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs2688198	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2688201	1.00[TSI][hapmap]
rs2688208	1.00[CHB][hapmap]
rs28372688	0.86[ASN][1000 genomes]
rs348739	1.00[TSI][hapmap]
rs348750	1.00[TSI][hapmap]
rs348752	1.00[TSI][hapmap]
rs3776984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39614	1.00[TSI][hapmap]
rs4452598	0.86[EUR][1000 genomes]
rs4626377	0.86[EUR][1000 genomes]
rs55692274	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56773390	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56895891	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61145644	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580123	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871813	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6895588	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6895702	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6895741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6895742	0.81[AMR][1000 genomes]
rs702742	1.00[TSI][hapmap]
rs73806917	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807206	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807207	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807213	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807216	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73809507	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709899	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7716019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816717	1.00[TSI][hapmap]
rs816718	1.00[CHB][hapmap];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	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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
2	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
3	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:154210200-154229000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:154210800-154229000	Weak transcription	Fetal Kidney	kidney
6	chr5:154210800-154229800	Weak transcription	Fetal Thymus	thymus
7	chr5:154211400-154228800	Weak transcription	Fetal Brain Female	brain
8	chr5:154211400-154229400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:154211400-154229400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:154211400-154229800	Weak transcription	Pancreas	Pancrea
11	chr5:154211400-154235800	Weak transcription	Dnd41	blood
12	chr5:154211800-154229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:154211800-154229200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:154212400-154229200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:154212600-154229400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:154214600-154229200	Weak transcription	Esophagus	oesophagus
17	chr5:154214600-154229400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:154214600-154229800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:154214800-154229400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:154214800-154230000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:154214800-154236400	Weak transcription	GM12878-XiMat	blood
22	chr5:154215000-154229000	Weak transcription	NHLF	lung
23	chr5:154215000-154229800	Weak transcription	Placenta	Placenta
24	chr5:154215200-154228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:154215200-154228800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:154215200-154229200	Weak transcription	Colonic Mucosa	Colon
27	chr5:154215200-154236400	Weak transcription	A549	lung
28	chr5:154215800-154228800	Weak transcription	Osteobl	bone
29	chr5:154215800-154229400	Weak transcription	HMEC	breast
30	chr5:154215800-154229800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:154216000-154227800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:154216000-154229000	Weak transcription	NHDF-Ad	bronchial
33	chr5:154216000-154229800	Weak transcription	NHEK	skin
34	chr5:154217600-154228800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:154217600-154229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:154217600-154229800	Weak transcription	Gastric	stomach
37	chr5:154217800-154226600	Weak transcription	Ovary	ovary
38	chr5:154217800-154227800	Weak transcription	Adipose Nuclei	Adipose
39	chr5:154217800-154228800	Weak transcription	Aorta	Aorta
40	chr5:154217800-154229000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:154217800-154229000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:154217800-154229000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:154217800-154229000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:154217800-154229200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:154217800-154229400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:154217800-154229400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr5:154217800-154229800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:154217800-154230200	Weak transcription	Spleen	Spleen
49	chr5:154218000-154227600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:154218000-154228800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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