Variant report

Variant	rs10478422
Chromosome Location	chr5:118747441-118747442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:118738573..118740948-chr5:118745923..118747452,2	K562	blood:
2	chr5:118322603..118326136-chr5:118745091..118748767,5	MCF-7	breast:
3	chr5:118323616..118324642-chr5:118747407..118748119,4	MCF-7	breast:
4	chr5:118745362..118747706-chr5:118750248..118751868,2	K562	blood:
5	chr5:118651201..118652914-chr5:118746753..118748686,2	K562	blood:
6	chr5:118648170..118648715-chr5:118747416..118748172,2	K562	blood:
7	chr5:118357310..118358382-chr5:118747153..118748053,5	MCF-7	breast:
8	chr5:118323682..118324344-chr5:118747438..118748180,2	Hela-S3	cervix:
9	chr5:118604013..118605667-chr5:118746438..118748354,2	MCF-7	breast:
10	chr5:118323688..118325465-chr5:118745878..118747588,2	MCF-7	breast:
11	chr5:118747162..118749496-chr5:118752473..118755239,2	K562	blood:
12	chr5:118602609..118607395-chr5:118746240..118749056,4	MCF-7	breast:
13	chr5:118323105..118324704-chr5:118747352..118748403,7	K562	blood:
14	chr5:118746206..118749496-chr5:118750368..118755239,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169570	Chromatin interaction
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10077888	0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1047322	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10478421	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1105769	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1105770	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11205	0.91[CHB][hapmap]
rs11241507	0.90[CHB][hapmap]
rs1155777	0.90[CHB][hapmap]
rs11949608	0.85[CHB][hapmap]
rs1490756	0.86[CHB][hapmap];0.83[GIH][hapmap]
rs1509144	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs150938	0.90[CHB][hapmap]
rs154632	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs165995	0.89[CHB][hapmap]
rs17145464	0.86[CHB][hapmap]
rs1848554	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs193346	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1995794	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2455466	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2455467	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2457222	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs250302	0.80[JPT][hapmap]
rs250303	0.85[JPT][hapmap]
rs257969	0.86[CHB][hapmap];0.80[GIH][hapmap]
rs257985	0.90[CHB][hapmap]
rs258047	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs258050	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs258051	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2914210	0.91[CHB][hapmap];0.80[GIH][hapmap]
rs32654	0.80[JPT][hapmap]
rs3733855	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797368	0.95[CHB][hapmap];0.86[GIH][hapmap]
rs3797372	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs3813309	0.80[JPT][hapmap]
rs3822527	0.85[CHB][hapmap]
rs455991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874848	0.85[JPT][hapmap]
rs6888436	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6888463	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6893184	0.91[EUR][1000 genomes]
rs7716785	0.94[CHB][hapmap]
rs7721752	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs924623	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv965533	chr5:118738884-118762384	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118707600-118754600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:118723000-118747600	Weak transcription	Pancreas	Pancrea
3	chr5:118745200-118747600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:118746200-118747600	Enhancers	Stomach Mucosa	stomach
5	chr5:118746400-118747600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:118746800-118747600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr5:118747000-118747600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:118747000-118747600	Weak transcription	Esophagus	oesophagus
9	chr5:118747000-118747600	Enhancers	Small Intestine	intestine
10	chr5:118747000-118748000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:118747000-118748000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:118747000-118748000	Active TSS	NHDF-Ad	bronchial
13	chr5:118747200-118747600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:118747200-118747600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:118747200-118747600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:118747200-118747600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:118747200-118747600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:118747200-118747600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr5:118747200-118747600	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr5:118747200-118747600	Enhancers	Fetal Brain Male	brain
21	chr5:118747200-118747800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr5:118747200-118747800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:118747200-118748000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:118747200-118748000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:118747200-118748000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:118747200-118748000	Active TSS	Right Atrium	heart
27	chr5:118747200-118748000	Active TSS	Right Ventricle	heart
28	chr5:118747200-118748000	Active TSS	Stomach Smooth Muscle	stomach
29	chr5:118747200-118748000	Flanking Active TSS	Hela-S3	cervix
30	chr5:118747200-118748000	Active TSS	HSMM	muscle
31	chr5:118747200-118748000	Active TSS	Osteobl	bone
32	chr5:118747400-118747600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:118747400-118747600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:118747400-118747600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr5:118747400-118747600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr5:118747400-118747600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:118747400-118747600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr5:118747400-118747600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr5:118747400-118747600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:118747400-118747600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr5:118747400-118747600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:118747400-118747600	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr5:118747400-118747600	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr5:118747400-118747600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr5:118747400-118747600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr5:118747400-118747600	Flanking Active TSS	Fetal Brain Female	brain
47	chr5:118747400-118747600	Flanking Active TSS	Fetal Heart	heart
48	chr5:118747400-118747600	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr5:118747400-118747600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
50	chr5:118747400-118747600	Enhancers	Dnd41	blood

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