Variant report

Variant	rs17166428
Chromosome Location	chr5:98229104-98229105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98221878..98225421-chr5:98228419..98230512,3	K562	blood:

Variant related genes	Relation type
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10039507	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10041263	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10041335	0.83[EUR][1000 genomes]
rs10055595	0.83[EUR][1000 genomes]
rs10056842	0.83[EUR][1000 genomes]
rs10056918	0.83[EUR][1000 genomes]
rs10061406	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10064594	0.81[EUR][1000 genomes]
rs10065808	0.83[EUR][1000 genomes]
rs10067635	0.83[EUR][1000 genomes]
rs10067866	0.83[EUR][1000 genomes]
rs10068003	0.83[EUR][1000 genomes]
rs10068917	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10077697	1.00[CEU][hapmap]
rs10085106	1.00[CEU][hapmap]
rs10085145	1.00[CEU][hapmap]
rs10515284	1.00[CEU][hapmap]
rs11948998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952820	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11953096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956636	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11958835	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332280	0.83[EUR][1000 genomes]
rs12332340	0.83[EUR][1000 genomes]
rs12332364	0.81[EUR][1000 genomes]
rs12332383	0.83[EUR][1000 genomes]
rs150992	0.83[LWK][hapmap]
rs161742	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs161747	1.00[CHD][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap]
rs161938	1.00[CHD][hapmap]
rs161941	1.00[CHD][hapmap]
rs161950	1.00[CHD][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap]
rs161952	1.00[CHD][hapmap]
rs162150	1.00[CHD][hapmap]
rs17166414	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17166423	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17166439	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17166455	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs17166484	0.87[EUR][1000 genomes]
rs17166575	0.83[EUR][1000 genomes]
rs17166578	0.89[CEU][hapmap];1.00[GIH][hapmap]
rs17663317	1.00[CEU][hapmap]
rs2164986	0.93[EUR][1000 genomes]
rs2617507	0.80[AFR][1000 genomes]
rs2963709	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3179904	1.00[CEU][hapmap]
rs326468	1.00[CHD][hapmap]
rs327810	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330419	1.00[CHD][hapmap]
rs36011435	0.93[EUR][1000 genomes]
rs44070	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55780476	0.83[EUR][1000 genomes]
rs55821667	0.83[EUR][1000 genomes]
rs55854720	0.81[EUR][1000 genomes]
rs55862038	0.81[ASN][1000 genomes]
rs56086412	0.83[EUR][1000 genomes]
rs56096102	0.81[EUR][1000 genomes]
rs56115002	0.83[EUR][1000 genomes]
rs56153113	0.83[EUR][1000 genomes]
rs56159022	0.81[EUR][1000 genomes]
rs56160758	0.83[EUR][1000 genomes]
rs56232429	0.81[EUR][1000 genomes]
rs56331326	0.89[EUR][1000 genomes]
rs56331947	0.87[EUR][1000 genomes]
rs56400831	0.93[EUR][1000 genomes]
rs56898185	0.81[ASN][1000 genomes]
rs58224759	0.81[ASN][1000 genomes]
rs58479016	0.83[EUR][1000 genomes]
rs59181854	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59325325	0.81[ASN][1000 genomes]
rs61199566	0.81[ASN][1000 genomes]
rs6596551	0.81[ASN][1000 genomes]
rs6866527	1.00[CEU][hapmap]
rs6866629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880359	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883467	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6890358	0.83[EUR][1000 genomes]
rs6893282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6895358	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs692832	1.00[CHD][hapmap]
rs727637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776004	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776005	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776017	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776026	1.00[ASN][1000 genomes]
rs73776027	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73776028	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73776032	1.00[ASN][1000 genomes]
rs7708436	0.87[EUR][1000 genomes]
rs7726329	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7737402	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs9327950	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9327954	0.83[EUR][1000 genomes]
rs9327955	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98188400-98247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:98189600-98241000	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:98189800-98241000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:98189800-98241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:98189800-98241400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:98189800-98241800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:98190000-98240600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:98190000-98240800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr5:98190000-98240800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:98190200-98240600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:98190200-98240600	Strong transcription	Liver	Liver
12	chr5:98190200-98241000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:98190400-98234600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:98190400-98238200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:98190400-98238800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:98190400-98240000	Weak transcription	Stomach Mucosa	stomach
17	chr5:98190400-98240400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:98190400-98240600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr5:98190400-98240800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr5:98190400-98241200	Strong transcription	Fetal Thymus	thymus
21	chr5:98190400-98243800	Strong transcription	Dnd41	blood
22	chr5:98190600-98240600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:98190600-98240800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:98190600-98240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:98190600-98241000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:98190800-98240000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:98191000-98240800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:98195200-98240800	Strong transcription	Primary B cells from cord blood	blood
29	chr5:98196200-98234000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:98198400-98240800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:98200000-98263000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:98200200-98240400	Strong transcription	HSMM	muscle
33	chr5:98200600-98240800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr5:98203000-98238200	Strong transcription	HUVEC	blood vessel
35	chr5:98203800-98238800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:98204400-98231200	Weak transcription	Right Ventricle	heart
37	chr5:98204600-98231200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:98207800-98240000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:98209400-98234000	Weak transcription	Fetal Brain Male	brain
40	chr5:98210000-98232200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:98210400-98238200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:98211200-98232200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr5:98211400-98241200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:98212000-98232200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:98212000-98236800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:98212000-98237200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:98214000-98230200	Strong transcription	GM12878-XiMat	blood
48	chr5:98214400-98234000	Weak transcription	Psoas Muscle	Psoas
49	chr5:98215000-98234400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:98215000-98263000	Weak transcription	Esophagus	oesophagus

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