Variant report

Variant	rs16860377
Chromosome Location	chr2:173305040-173305041
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	chr2:173290118..173293854-chr2:173304445..173308429,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091409	Chromatin interaction
ENSG00000226963	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10171775	0.98[ASN][1000 genomes]
rs10175670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10184567	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10195932	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10197251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076595	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12465295	0.82[JPT][hapmap]
rs12465442	0.81[JPT][hapmap]
rs12467358	0.82[JPT][hapmap]
rs12469875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12473999	0.80[ASN][1000 genomes]
rs12477247	0.81[JPT][hapmap]
rs12477594	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12478465	0.82[JPT][hapmap]
rs12622044	0.91[ASN][1000 genomes]
rs2293646	0.82[JPT][hapmap]
rs2357415	0.82[JPT][hapmap]
rs28464102	0.83[ASN][1000 genomes]
rs28540552	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3762619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3792260	0.82[JPT][hapmap]
rs3934627	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4281870	0.96[ASN][1000 genomes]
rs4480959	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4993282	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4993283	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6718477	0.82[JPT][hapmap]
rs6721597	0.84[ASN][1000 genomes]
rs6755100	0.82[JPT][hapmap]
rs7567159	0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7604441	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs9711634	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294800-173306400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
3	chr2:173295200-173306600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:173295200-173306600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
6	chr2:173296000-173305600	Weak transcription	Fetal Lung	lung
7	chr2:173296000-173307600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr2:173296200-173307600	Enhancers	Fetal Thymus	thymus
9	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:173297000-173306600	Enhancers	Small Intestine	intestine
11	chr2:173297000-173307600	Enhancers	Pancreas	Pancrea
12	chr2:173297600-173307400	Enhancers	Spleen	Spleen
13	chr2:173300200-173307600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:173300400-173308000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:173300600-173306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:173301000-173308400	Enhancers	Fetal Intestine Small	intestine
17	chr2:173301200-173305600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:173301200-173305800	Weak transcription	Fetal Heart	heart
19	chr2:173301200-173308400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:173301400-173308400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr2:173301600-173305400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:173301800-173305600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:173301800-173305800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:173302400-173307600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr2:173302400-173308200	Enhancers	HepG2	liver
26	chr2:173302600-173308000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:173303000-173305200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr2:173303000-173305400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr2:173303000-173305600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:173303000-173305800	Enhancers	Brain Anterior Caudate	brain
31	chr2:173303200-173305600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr2:173303200-173305600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:173303200-173305600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:173303200-173307600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:173303200-173308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:173303200-173309600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:173303400-173305200	Weak transcription	GM12878-XiMat	blood
38	chr2:173303400-173305600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:173303400-173305800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:173303400-173306400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:173303600-173305200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:173303600-173305600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:173303600-173307600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:173303800-173305600	Enhancers	Thymus	Thymus
45	chr2:173303800-173305800	Enhancers	Right Ventricle	heart
46	chr2:173303800-173306000	Weak transcription	Placenta	Placenta
47	chr2:173303800-173306600	Enhancers	HSMMtube	muscle
48	chr2:173303800-173307600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:173304000-173305400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:173304000-173305800	Enhancers	Adipose Nuclei	Adipose

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