Variant report

Variant	rs16860397
Chromosome Location	chr2:173308194-173308195
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173290118..173293854-chr2:173304445..173308429,5	MCF-7	breast:
2	chr2:173297263..173301573-chr2:173305902..173308346,3	MCF-7	breast:
3	chr2:173305610..173308515-chr2:173310023..173312671,2	MCF-7	breast:
4	chr2:173307073..173308885-chr2:173311042..173312605,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226963	Chromatin interaction
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	1.00[EUR][1000 genomes]
rs10207640	1.00[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10207654	1.00[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10210544	0.85[JPT][hapmap]
rs10930559	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12052385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12053442	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12615596	0.96[EUR][1000 genomes]
rs12621278	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12622724	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs13410475	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1574256	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1574259	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16860416	0.84[JPT][hapmap]
rs16860419	0.87[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16860426	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860438	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[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];0.85[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs28485589	0.90[EUR][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs4405725	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56892098	0.90[EUR][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57878744	0.90[EUR][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59454075	1.00[EUR][1000 genomes]
rs59970483	0.85[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6730284	0.85[EUR][1000 genomes]
rs6741759	0.85[EUR][1000 genomes]
rs9636257	1.00[AFR][1000 genomes];0.85[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	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
2	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
2	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
3	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr2:173301000-173308400	Enhancers	Fetal Intestine Small	intestine
5	chr2:173301200-173308400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:173301400-173308400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr2:173302400-173308200	Enhancers	HepG2	liver
8	chr2:173303200-173308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:173303200-173309600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:173304200-173311400	Weak transcription	Liver	Liver
11	chr2:173304600-173308400	Enhancers	HSMM	muscle
12	chr2:173304600-173308800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:173304600-173310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:173304800-173308800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:173305000-173310400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:173305400-173308200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:173305400-173309000	Enhancers	Fetal Muscle Leg	muscle
19	chr2:173305800-173308800	Enhancers	Fetal Heart	heart
20	chr2:173306000-173308400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:173306200-173308200	Enhancers	Thymus	Thymus
22	chr2:173306200-173310400	Weak transcription	Fetal Lung	lung
23	chr2:173306200-173311200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:173306600-173308200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:173306800-173309800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:173306800-173311400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:173307000-173308400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:173307000-173308600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr2:173307000-173308600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:173307000-173308600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr2:173307000-173309600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:173307000-173309600	Weak transcription	Brain Germinal Matrix	brain
34	chr2:173307000-173310600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:173307200-173308400	Enhancers	HSMMtube	muscle
36	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:173307400-173308200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:173307400-173308200	Enhancers	HMEC	breast
39	chr2:173307400-173308400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:173307400-173308400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:173307400-173310400	Weak transcription	Brain Substantia Nigra	brain
42	chr2:173307400-173310400	Weak transcription	Gastric	stomach
43	chr2:173307400-173310400	Weak transcription	Spleen	Spleen
44	chr2:173307400-173310400	Weak transcription	NHLF	lung
45	chr2:173307400-173310600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:173307400-173312800	Weak transcription	Fetal Kidney	kidney
47	chr2:173307400-173313600	Weak transcription	Placenta	Placenta
48	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:173307600-173308200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:173307600-173308400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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