Variant report

Variant	rs16860426
Chromosome Location	chr2:173319112-173319113
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173317241..173319524-chr2:173329311..173331759,2	K562	blood:
2	chr2:173278303..173281188-chr2:173318534..173320264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232788	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10207640	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10207654	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10210544	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10930559	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12052385	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12053442	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12615596	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622724	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13387602	0.83[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13421350	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1574256	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16860397	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860416	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16860419	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860438	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16860634	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28485589	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4405725	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56892098	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs57878744	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59454075	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59970483	0.82[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6726739	1.00[JPT][hapmap]
rs6730284	0.82[EUR][1000 genomes]
rs6741759	0.82[EUR][1000 genomes]
rs7564416	1.00[JPT][hapmap]
rs9636257	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:173307600-173321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:173310800-173319800	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:173310800-173320000	Weak transcription	Lung	lung
5	chr2:173310800-173322400	Weak transcription	Thymus	Thymus
6	chr2:173311600-173319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:173311600-173319200	Weak transcription	HUVEC	blood vessel
8	chr2:173311800-173319200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:173312200-173319400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:173312200-173323600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:173312400-173319200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:173313200-173319800	Weak transcription	Fetal Kidney	kidney
13	chr2:173313600-173323400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:173313800-173319200	Weak transcription	HepG2	liver
15	chr2:173314200-173319200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:173314200-173319200	Weak transcription	Hela-S3	cervix
17	chr2:173314400-173319400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:173315000-173320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:173315000-173320800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:173315200-173319400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:173315200-173324800	Genic enhancers	NHEK	skin
22	chr2:173315400-173319800	Weak transcription	HSMM	muscle
23	chr2:173315400-173320200	Weak transcription	HSMMtube	muscle
24	chr2:173316000-173320400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:173316000-173320800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:173316000-173322800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:173316200-173320800	Genic enhancers	HMEC	breast
28	chr2:173316200-173321800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:173316200-173321800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr2:173316200-173323400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:173316200-173323800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:173316400-173319400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:173316400-173319600	Enhancers	Spleen	Spleen
34	chr2:173316400-173321400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:173316600-173319600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:173317000-173322000	Genic enhancers	Primary T cells from cord blood	blood
37	chr2:173317000-173323800	Enhancers	Stomach Mucosa	stomach
38	chr2:173317200-173319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:173317200-173319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:173317200-173322600	Weak transcription	Brain Anterior Caudate	brain
41	chr2:173317200-173325400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:173317400-173319600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:173317400-173319600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:173317400-173320000	Weak transcription	Left Ventricle	heart
45	chr2:173317600-173319200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:173317600-173319400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:173317600-173320800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:173317600-173326000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:173317600-173326000	Weak transcription	Brain Substantia Nigra	brain
50	chr2:173317800-173319200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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