Variant report

Variant	rs11898704
Chromosome Location	chr2:39602950-39602951
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	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10490305	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886110	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11886434	0.82[AFR][1000 genomes]
rs11895366	0.87[AFR][1000 genomes]
rs11902188	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17023620	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17038958	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708227	1.00[JPT][hapmap]
rs3770661	0.83[ASN][1000 genomes]
rs55797011	0.92[ASN][1000 genomes]
rs55961227	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56361338	0.83[ASN][1000 genomes]
rs56850142	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56928728	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57084694	0.81[AFR][1000 genomes]
rs58005382	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58824151	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59459399	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59707152	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59896787	0.81[AFR][1000 genomes]
rs60394429	0.90[AFR][1000 genomes]
rs61219633	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6544206	1.00[JPT][hapmap]
rs6544225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6712399	1.00[ASW][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6723987	0.93[AFR][1000 genomes]
rs6725784	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6727395	1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6731330	1.00[JPT][hapmap]
rs6751506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73923836	0.83[ASN][1000 genomes]
rs73923844	0.86[AFR][1000 genomes]
rs73923848	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73923887	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73923888	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73923889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73923895	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73924016	0.81[AFR][1000 genomes]
rs73924810	0.83[ASN][1000 genomes]
rs73924815	0.83[ASN][1000 genomes]
rs73924816	0.83[ASN][1000 genomes]
rs73924817	0.83[ASN][1000 genomes]
rs73924818	0.83[ASN][1000 genomes]
rs7565210	0.87[AFR][1000 genomes]
rs7591563	0.92[AFR][1000 genomes]
rs7595047	0.83[ASN][1000 genomes]
rs7595102	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7599017	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39584400-39604600	Weak transcription	Right Ventricle	heart
2	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
3	chr2:39587200-39604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:39587800-39604800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39588000-39607800	Weak transcription	Ovary	ovary
6	chr2:39588000-39608800	Weak transcription	Lung	lung
7	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
9	chr2:39588200-39603000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:39588400-39603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:39590000-39604800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:39590200-39604800	Weak transcription	HSMMtube	muscle
13	chr2:39591800-39604600	Weak transcription	NH-A	brain
14	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:39592000-39606800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:39592400-39604600	Weak transcription	Fetal Heart	heart
17	chr2:39592600-39607000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39593400-39603200	Weak transcription	K562	blood
20	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
21	chr2:39595800-39604600	Weak transcription	Psoas Muscle	Psoas
22	chr2:39595800-39606800	Weak transcription	HUVEC	blood vessel
23	chr2:39595800-39607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:39596200-39605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:39596400-39604600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:39596400-39605000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:39596400-39606800	Weak transcription	Fetal Brain Male	brain
28	chr2:39596800-39604000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:39596800-39605600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:39597200-39607800	Weak transcription	Small Intestine	intestine
31	chr2:39597600-39603000	Weak transcription	NHLF	lung
32	chr2:39597600-39604400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:39597600-39604800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:39597600-39605600	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:39597600-39606200	Weak transcription	Brain Anterior Caudate	brain
36	chr2:39597600-39606200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:39598600-39606400	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:39598800-39604600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:39599200-39603000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:39599400-39603600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:39599600-39603400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:39599600-39603800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:39599800-39603600	Strong transcription	HSMM	muscle
44	chr2:39599800-39604000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:39600000-39606400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:39600200-39603600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:39600600-39603400	Strong transcription	HepG2	liver
48	chr2:39600600-39606800	Weak transcription	Fetal Kidney	kidney
49	chr2:39600600-39614600	Weak transcription	Aorta	Aorta
50	chr2:39600800-39603400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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