Variant report

Variant	rs10010375
Chromosome Location	chr4:3041476-3041477
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	chr4:2963384..2966689-chr4:3039150..3042099,3	MCF-7	breast:
2	chr4:2962324..2965157-chr4:3038658..3041548,2	K562	blood:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10000252	1.00[CEU][hapmap]
rs10002065	1.00[CEU][hapmap]
rs10009229	1.00[CEU][hapmap]
rs10009935	1.00[CEU][hapmap]
rs10011127	1.00[CEU][hapmap]
rs10011412	1.00[CEU][hapmap]
rs10014333	1.00[CEU][hapmap]
rs10016755	1.00[CEU][hapmap]
rs1419036	1.00[CEU][hapmap]
rs16843503	1.00[JPT][hapmap]
rs16843866	1.00[CEU][hapmap]
rs16843869	1.00[CEU][hapmap]
rs2471343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2471348	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2488811	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2515931	1.00[CEU][hapmap]
rs2515934	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2515955	0.89[EUR][1000 genomes]
rs2515956	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28795684	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28856696	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2960299	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2995802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs3021124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs363138	1.00[CEU][hapmap]
rs61269488	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7693317	1.00[CEU][hapmap]
rs9291159	1.00[CEU][hapmap]
rs9991144	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
2	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
3	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
6	chr4:3038400-3042600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:3038600-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:3039400-3042800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:3039400-3043000	Weak transcription	Pancreas	Pancrea
10	chr4:3039600-3042800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:3039800-3043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:3039800-3043000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:3039800-3043200	Weak transcription	Fetal Kidney	kidney
14	chr4:3040000-3042200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:3040000-3042400	Weak transcription	Spleen	Spleen
16	chr4:3040000-3042600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:3040000-3043000	Weak transcription	Psoas Muscle	Psoas
18	chr4:3040000-3043000	Weak transcription	Right Atrium	heart
19	chr4:3040200-3041600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:3040200-3041800	Enhancers	Primary B cells from peripheral blood	blood
21	chr4:3040200-3042400	Weak transcription	Colonic Mucosa	Colon
22	chr4:3040200-3042400	Weak transcription	Placenta	Placenta
23	chr4:3040200-3042600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:3040200-3042800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:3040200-3042800	Weak transcription	Liver	Liver
26	chr4:3040200-3042800	Weak transcription	Brain Anterior Caudate	brain
27	chr4:3040200-3042800	Weak transcription	NHLF	lung
28	chr4:3040200-3043000	Weak transcription	Brain Substantia Nigra	brain
29	chr4:3040200-3043000	Weak transcription	Right Ventricle	heart
30	chr4:3040200-3043200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:3040400-3042200	Enhancers	Primary B cells from cord blood	blood
32	chr4:3040400-3042400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:3040400-3042600	Weak transcription	Adipose Nuclei	Adipose
34	chr4:3040400-3042800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:3040400-3042800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:3040400-3042800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:3040400-3042800	Weak transcription	Osteobl	bone
38	chr4:3040600-3041600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:3040600-3041600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:3040600-3041600	Enhancers	GM12878-XiMat	blood
41	chr4:3040600-3042200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:3040600-3042400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:3040600-3042400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:3040600-3042400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:3040600-3042400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:3040600-3042400	Weak transcription	NHDF-Ad	bronchial
47	chr4:3040600-3042600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:3040600-3042600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:3040600-3042600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:3040600-3042600	Weak transcription	Esophagus	oesophagus

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