Variant report

Variant	rs12650202
Chromosome Location	chr4:48692771-48692772
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48691449..48693997-chr4:48694724..48696610,2	MCF-7	breast:
2	chr4:48685624..48689755-chr4:48691004..48694286,4	K562	blood:
3	chr4:48689938..48695241-chr4:48778784..48782766,5	MCF-7	breast:
4	chr4:48691459..48694072-chr4:48776269..48778861,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10433725	1.00[AMR][1000 genomes]
rs10938540	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12499963	0.81[AFR][1000 genomes]
rs1546653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1949423	1.00[AMR][1000 genomes]
rs2056197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2056200	1.00[AMR][1000 genomes]
rs2138868	1.00[AMR][1000 genomes]
rs2354313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2354315	1.00[AMR][1000 genomes]
rs6845398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7436127	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7667909	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7690793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs938789	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1796692	chr4:48686817-48726266	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48663600-48700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:48670200-48700000	Weak transcription	Esophagus	oesophagus
4	chr4:48670200-48702000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:48670200-48702000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:48670400-48696000	Weak transcription	Left Ventricle	heart
7	chr4:48671400-48696000	Weak transcription	Right Ventricle	heart
8	chr4:48679000-48700000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:48680200-48692800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:48680600-48699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:48683400-48699600	Weak transcription	Psoas Muscle	Psoas
12	chr4:48683600-48700000	Weak transcription	Fetal Intestine Large	intestine
13	chr4:48683600-48700400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:48684000-48698400	Weak transcription	NHEK	skin
15	chr4:48684200-48695400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:48685000-48700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:48686400-48694200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:48686400-48699600	Weak transcription	Placenta	Placenta
19	chr4:48686400-48700000	Weak transcription	Dnd41	blood
20	chr4:48686600-48693200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:48686600-48694000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:48686600-48694200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:48686800-48695000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:48686800-48700200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:48686800-48708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:48687000-48693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:48687000-48700000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:48687000-48700000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:48687000-48701000	Weak transcription	GM12878-XiMat	blood
30	chr4:48687000-48708400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:48687200-48700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:48687200-48708400	Weak transcription	Primary B cells from cord blood	blood
33	chr4:48688800-48696000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:48689000-48694200	Weak transcription	Brain Angular Gyrus	brain
35	chr4:48689400-48693000	Weak transcription	Fetal Kidney	kidney
36	chr4:48689800-48694200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:48689800-48694400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:48690000-48693000	Weak transcription	Brain Anterior Caudate	brain
39	chr4:48690000-48693000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:48690000-48693600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr4:48690000-48694200	Weak transcription	Primary T cells from cord blood	blood
42	chr4:48690000-48694600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr4:48690000-48694800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:48690200-48693000	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:48690200-48694000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:48690200-48694200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:48690200-48694800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:48690200-48705200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:48690400-48693000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:48690400-48700000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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