Variant report

Variant	rs7559217
Chromosome Location	chr2:153324632-153324633
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	chr2:153190311..153192513-chr2:153322864..153325186,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157827	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10173899	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10179418	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs10180542	0.90[ASN][1000 genomes]
rs10194603	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10208776	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10432493	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12616906	0.89[ASN][1000 genomes]
rs12693378	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13386403	0.80[JPT][hapmap]
rs13390698	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13424038	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13427076	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs13427990	0.86[ASN][1000 genomes]
rs16831169	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16831174	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2078444	0.92[ASN][1000 genomes]
rs2346205	0.81[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2346209	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2881339	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4143274	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4146259	0.94[JPT][hapmap]
rs4664587	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4664589	0.87[ASN][1000 genomes]
rs4664590	0.87[ASN][1000 genomes]
rs58121347	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59965317	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6434059	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6434060	0.86[ASN][1000 genomes]
rs6434061	0.88[ASN][1000 genomes]
rs6434062	0.86[ASN][1000 genomes]
rs6725661	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6737699	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6747765	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs6748954	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73002264	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73968029	0.91[ASN][1000 genomes]
rs7582984	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7586195	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7587794	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7590207	0.88[ASN][1000 genomes]
rs7592283	0.89[ASN][1000 genomes]
rs7593411	0.84[ASN][1000 genomes]
rs7594969	0.83[ASN][1000 genomes]
rs7606592	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2830258	chr2:153318339-153349165	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153317400-153328000	Enhancers	Brain Substantia Nigra	brain
2	chr2:153318400-153327200	Enhancers	HepG2	liver
3	chr2:153319200-153325000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:153319400-153325600	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:153320200-153325600	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr2:153320600-153325000	Enhancers	Psoas Muscle	Psoas
7	chr2:153320600-153328400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:153320800-153329400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:153320800-153331600	Enhancers	Hela-S3	cervix
10	chr2:153321000-153326200	Enhancers	Fetal Lung	lung
11	chr2:153321000-153329600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:153321200-153325400	Enhancers	A549	lung
13	chr2:153321200-153326400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:153321200-153326800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:153321400-153324800	Enhancers	Aorta	Aorta
16	chr2:153321400-153326200	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:153321600-153324800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:153321600-153324800	Enhancers	Fetal Stomach	stomach
19	chr2:153321600-153325000	Enhancers	HMEC	breast
20	chr2:153321600-153326800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:153321800-153325400	Enhancers	Adipose Nuclei	Adipose
22	chr2:153321800-153325600	Enhancers	Brain Anterior Caudate	brain
23	chr2:153322000-153324800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:153322000-153325200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:153322000-153325200	Weak transcription	HUVEC	blood vessel
26	chr2:153322000-153325600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:153322000-153325600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:153322200-153324800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:153322200-153325400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:153322400-153325600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:153322400-153326800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:153322600-153325000	Enhancers	Colon Smooth Muscle	Colon
33	chr2:153322600-153325400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:153322600-153326200	Enhancers	Primary B cells from cord blood	blood
35	chr2:153322800-153325800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:153322800-153329200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:153323000-153326000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr2:153323200-153324800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr2:153323200-153325400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:153323200-153325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:153323200-153326200	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:153323200-153326600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr2:153323400-153324800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:153323400-153324800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:153323400-153325200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:153323400-153325400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:153323400-153326000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:153323400-153326200	Enhancers	H1 Cell Line	embryonic stem cell
49	chr2:153323400-153326200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:153323600-153325600	Enhancers	Stomach Mucosa	stomach

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