Variant report

Variant	rs4973563
Chromosome Location	chr2:233716421-233716422
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	chr2:233715218..233716776-chr2:233729357..233731524,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1078323	0.96[CEU][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10933406	0.93[CEU][hapmap]
rs1104764	0.89[CEU][hapmap]
rs11688166	1.00[CEU][hapmap]
rs11689851	1.00[CEU][hapmap]
rs12105766	0.92[CEU][hapmap]
rs12619195	0.93[CEU][hapmap]
rs12993791	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13001052	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13007579	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13008436	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13009957	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021823	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13024330	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164	1.00[CEU][hapmap]
rs1973675	0.92[CEU][hapmap]
rs2289911	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2344613	1.00[CEU][hapmap]
rs2675972	0.82[EUR][1000 genomes]
rs283470	0.93[CEU][hapmap]
rs34707169	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35491427	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4973564	0.88[CEU][hapmap]
rs6704763	0.92[CEU][hapmap]
rs6717048	0.93[CEU][hapmap]
rs6733495	0.93[CEU][hapmap]
rs737027	0.92[CEU][hapmap]
rs7560115	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778341	0.90[ASN][1000 genomes]
rs778371	0.96[ASN][1000 genomes]
rs921055	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:233691200-233717200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:233698400-233723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:233699200-233717000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:233699800-233717000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr2:233701800-233717000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:233703400-233716600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:233703400-233717000	Strong transcription	Placenta	Placenta
12	chr2:233703400-233718600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:233703400-233726400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:233703400-233726600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:233703600-233717200	Strong transcription	Thymus	Thymus
16	chr2:233703600-233718400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:233703600-233725200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:233703800-233716800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:233703800-233717000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:233703800-233717000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:233703800-233717200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:233703800-233724800	Strong transcription	Dnd41	blood
23	chr2:233704000-233717000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:233704000-233717200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:233704000-233721400	Strong transcription	Fetal Intestine Large	intestine
26	chr2:233704200-233716800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:233704200-233717000	Strong transcription	GM12878-XiMat	blood
28	chr2:233704200-233718200	Strong transcription	Fetal Brain Female	brain
29	chr2:233704200-233719200	Strong transcription	Fetal Muscle Leg	muscle
30	chr2:233704200-233725000	Strong transcription	Fetal Thymus	thymus
31	chr2:233704400-233716800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:233704400-233716800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:233704400-233717000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:233704400-233726200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:233704400-233726600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:233704600-233716800	Strong transcription	Rectal Smooth Muscle	rectum
37	chr2:233704600-233717000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr2:233704600-233717000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:233704600-233717200	Strong transcription	Adipose Nuclei	Adipose
40	chr2:233704600-233717600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:233704600-233717600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:233704600-233718200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:233704600-233726000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:233704600-233728000	Strong transcription	Primary T cells from cord blood	blood
45	chr2:233704800-233716800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:233704800-233719000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:233704800-233726600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:233705000-233717000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:233705000-233717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:233705000-233726600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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