Variant report

Variant	rs10938538
Chromosome Location	chr4:48694945-48694946
allele	C/T
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	chr4:48682494..48684841-chr4:48693088..48695162,2	K562	blood:
3	chr4:48689938..48695241-chr4:48778784..48782766,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10029425	1.00[AMR][1000 genomes]
rs10034207	1.00[AMR][1000 genomes]
rs10049760	1.00[AMR][1000 genomes]
rs10755182	1.00[AMR][1000 genomes]
rs10805171	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10805172	1.00[AMR][1000 genomes]
rs10938535	1.00[AMR][1000 genomes]
rs10938539	1.00[AMR][1000 genomes]
rs10938541	1.00[AMR][1000 genomes]
rs12500224	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12500244	1.00[AMR][1000 genomes]
rs12507475	1.00[AMR][1000 genomes]
rs12507546	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13125379	1.00[AMR][1000 genomes]
rs1474072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1517673	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1517676	1.00[AMR][1000 genomes]
rs1517677	1.00[AMR][1000 genomes]
rs1533511	1.00[AMR][1000 genomes]
rs1554257	1.00[AMR][1000 genomes]
rs1616561	1.00[AMR][1000 genomes]
rs1702796	1.00[AMR][1000 genomes]
rs1702799	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1712771	1.00[AMR][1000 genomes]
rs1949422	1.00[AMR][1000 genomes]
rs2138866	1.00[AMR][1000 genomes]
rs2138867	1.00[AMR][1000 genomes]
rs28371079	1.00[AMR][1000 genomes]
rs2883410	1.00[AMR][1000 genomes]
rs2940319	1.00[AMR][1000 genomes]
rs4235155	1.00[AMR][1000 genomes]
rs4235157	1.00[AMR][1000 genomes]
rs4235159	0.96[AFR][1000 genomes]
rs4330326	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4558842	1.00[AMR][1000 genomes]
rs4694896	1.00[AMR][1000 genomes]
rs4694898	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	1.00[AMR][1000 genomes]
rs4695386	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695390	1.00[AMR][1000 genomes]
rs4695402	1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs4998005	1.00[AMR][1000 genomes]
rs6447642	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	1.00[AMR][1000 genomes]
rs6447657	1.00[AMR][1000 genomes]
rs6821456	1.00[AMR][1000 genomes]
rs6823351	1.00[AMR][1000 genomes]
rs6827481	1.00[AMR][1000 genomes]
rs6828500	1.00[AMR][1000 genomes]
rs6835757	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844088	1.00[AMR][1000 genomes]
rs6846797	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6848222	1.00[AMR][1000 genomes]
rs6848417	1.00[AMR][1000 genomes]
rs6849798	1.00[AMR][1000 genomes]
rs6853876	1.00[AMR][1000 genomes]
rs707720	1.00[AMR][1000 genomes]
rs7434721	1.00[AMR][1000 genomes]
rs7664507	1.00[AMR][1000 genomes]
rs7689293	1.00[AMR][1000 genomes]
rs7689662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7692480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7698064	1.00[AMR][1000 genomes]
rs776581	1.00[AMR][1000 genomes]
rs776583	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776587	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776589	1.00[AMR][1000 genomes]
rs776595	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776603	1.00[AMR][1000 genomes]
rs938791	1.00[AMR][1000 genomes]
rs9994214	1.00[AMR][1000 genomes]
rs9997932	1.00[AMR][1000 genomes]
rs9998178	0.83[AFR][1000 genomes];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:72 , 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	chr4:48680600-48699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:48683400-48699600	Weak transcription	Psoas Muscle	Psoas
11	chr4:48683600-48700000	Weak transcription	Fetal Intestine Large	intestine
12	chr4:48683600-48700400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:48684000-48698400	Weak transcription	NHEK	skin
14	chr4:48684200-48695400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:48685000-48700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:48686400-48699600	Weak transcription	Placenta	Placenta
17	chr4:48686400-48700000	Weak transcription	Dnd41	blood
18	chr4:48686800-48695000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:48686800-48700200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:48686800-48708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:48687000-48700000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:48687000-48700000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:48687000-48701000	Weak transcription	GM12878-XiMat	blood
24	chr4:48687000-48708400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:48687200-48700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:48687200-48708400	Weak transcription	Primary B cells from cord blood	blood
27	chr4:48688800-48696000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:48690200-48705200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:48690400-48700000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:48691400-48700400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:48691600-48699600	Weak transcription	HSMM	muscle
32	chr4:48691600-48710400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:48691800-48700000	Weak transcription	Liver	Liver
34	chr4:48692400-48696000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:48692600-48700000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:48693000-48695200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:48693000-48695600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:48693200-48695000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:48693400-48695200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:48693600-48695000	Weak transcription	Brain Anterior Caudate	brain
41	chr4:48693600-48696800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:48693600-48700200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:48694000-48695200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:48694200-48695800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr4:48694200-48696000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr4:48694200-48696200	Enhancers	Brain Cingulate Gyrus	brain
47	chr4:48694200-48696600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr4:48694200-48697200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:48694200-48697200	Enhancers	Brain Angular Gyrus	brain
50	chr4:48694200-48698000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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