Variant report

Variant	rs16860438
Chromosome Location	chr2:173321413-173321414
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173111550..173113356-chr2:173319869..173321428,2	MCF-7	breast:
2	chr2:173320023..173322995-chr2:173325583..173327892,3	MCF-7	breast:
3	chr2:173320793..173322566-chr2:173325005..173326952,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10207640	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10207654	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208194	0.85[ASN][1000 genomes]
rs10210544	0.86[JPT][hapmap]
rs10930559	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10930561	0.85[CHB][hapmap]
rs12052253	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052385	1.00[CEU][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];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12615596	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621278	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12622724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13421350	0.93[JPT][hapmap]
rs1530864	0.85[CHB][hapmap]
rs1530865	0.85[CHB][hapmap]
rs1574256	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1574259	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860397	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860416	0.92[JPT][hapmap]
rs16860419	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860426	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];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16860513	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs16860515	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16860634	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16860643	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16860693	0.85[CHB][hapmap]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes]
rs2293648	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2357637	0.81[CHB][hapmap]
rs28485589	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28595036	0.85[ASN][1000 genomes]
rs35783685	0.82[ASN][1000 genomes]
rs35821653	0.82[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4405725	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56892098	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57878744	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59454075	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59476799	0.80[ASN][1000 genomes]
rs59970483	0.82[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6726739	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6730284	0.82[EUR][1000 genomes]
rs6741759	0.82[EUR][1000 genomes]
rs7564416	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9636257	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][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:87 , 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	chr2:173310800-173322400	Weak transcription	Thymus	Thymus
3	chr2:173312200-173323600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:173313600-173323400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:173315200-173324800	Genic enhancers	NHEK	skin
6	chr2:173316000-173322800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:173316200-173321800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:173316200-173321800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:173316200-173323400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:173316200-173323800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:173317000-173322000	Genic enhancers	Primary T cells from cord blood	blood
12	chr2:173317000-173323800	Enhancers	Stomach Mucosa	stomach
13	chr2:173317200-173322600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:173317200-173325400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:173317600-173326000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:173317600-173326000	Weak transcription	Brain Substantia Nigra	brain
17	chr2:173317800-173323000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:173318200-173322600	Weak transcription	Psoas Muscle	Psoas
19	chr2:173318400-173322600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:173318800-173326200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:173319000-173322000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr2:173319200-173330600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:173319600-173324800	Enhancers	Fetal Thymus	thymus
24	chr2:173319800-173321600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:173319800-173326400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:173320000-173325400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:173320200-173321600	Enhancers	HSMMtube	muscle
28	chr2:173320200-173326600	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:173320400-173324400	Weak transcription	HUVEC	blood vessel
30	chr2:173320600-173322000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:173320600-173327200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:173320800-173322000	Enhancers	Spleen	Spleen
33	chr2:173320800-173322200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:173320800-173325400	Enhancers	HMEC	breast
35	chr2:173320800-173326200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:173321000-173321600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:173321000-173324400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:173321000-173325400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:173321000-173326000	Weak transcription	HepG2	liver
40	chr2:173321000-173326400	Weak transcription	Right Ventricle	heart
41	chr2:173321000-173328000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:173321200-173322400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:173321200-173322400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:173321200-173323200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:173321200-173323200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:173321200-173324400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr2:173321200-173324400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:173321200-173324600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:173321200-173325200	Weak transcription	Hela-S3	cervix
50	chr2:173321200-173325400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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