Variant report

Variant	rs4405725
Chromosome Location	chr2:173305382-173305383
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	chr2:173290118..173293854-chr2:173304445..173308429,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091409	Chromatin interaction
ENSG00000226963	Chromatin interaction

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

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

rs_ID	r²[population]
rs10187564	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10207640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10207654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10210544	1.00[JPT][hapmap]
rs10930559	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052385	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs12053442	0.82[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12615584	0.82[EUR][1000 genomes]
rs12615596	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12621278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12622724	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13421350	0.93[JPT][hapmap]
rs1574256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1574259	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16860397	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs16860416	1.00[JPT][hapmap]
rs16860419	0.96[EUR][1000 genomes]
rs16860426	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]
rs16860438	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16860634	1.00[CEU][hapmap]
rs2293645	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap]
rs2293648	1.00[CEU][hapmap]
rs28485589	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55867175	0.82[EUR][1000 genomes]
rs56882727	0.82[EUR][1000 genomes]
rs56892098	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57244773	0.82[EUR][1000 genomes]
rs57404607	0.82[EUR][1000 genomes]
rs57587465	0.82[EUR][1000 genomes]
rs57878744	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59374567	0.82[EUR][1000 genomes]
rs59454075	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59476799	0.82[EUR][1000 genomes]
rs59970483	0.82[EUR][1000 genomes]
rs60096331	0.82[EUR][1000 genomes]
rs6726739	0.93[JPT][hapmap]
rs6730284	0.82[EUR][1000 genomes]
rs6741759	0.82[EUR][1000 genomes]
rs7564416	0.93[JPT][hapmap]
rs9636257	0.82[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	chr2:173303000-173305400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr2:173303000-173305600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:173303000-173305800	Enhancers	Brain Anterior Caudate	brain
30	chr2:173303200-173305600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:173303200-173305600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:173303200-173305600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:173303200-173307600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:173303200-173308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:173303200-173309600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:173303400-173305600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:173303400-173305800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:173303400-173306400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:173303600-173305600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:173303600-173307600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:173303800-173305600	Enhancers	Thymus	Thymus
42	chr2:173303800-173305800	Enhancers	Right Ventricle	heart
43	chr2:173303800-173306000	Weak transcription	Placenta	Placenta
44	chr2:173303800-173306600	Enhancers	HSMMtube	muscle
45	chr2:173303800-173307600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:173304000-173305400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:173304000-173305800	Enhancers	Adipose Nuclei	Adipose
48	chr2:173304000-173306000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:173304000-173306000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:173304000-173306400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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