Variant report

Variant	rs3824121
Chromosome Location	chr8:54754367-54754368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr8:54754349-54754556	K562	blood:	n/a	chr8:54754477-54754488 chr8:54754477-54754489 chr8:54754477-54754489 chr8:54754472-54754489
2	POLR2A	chr8:54754133-54754471	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:54754073..54757431-chr8:54763114..54767534,4	K562	blood:
2	chr8:54749963..54753631-chr8:54753914..54756219,5	MCF-7	breast:
3	chr8:54733544..54735901-chr8:54752993..54755423,2	MCF-7	breast:
4	chr8:53624816..53627483-chr8:54753343..54757526,4	K562	blood:

Variant related genes	Relation type
ATP6V1H	TF binding region
ENSG00000047249	Chromatin interaction
ENSG00000023287	Chromatin interaction
ENSG00000147509	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004228	1.00[CEU][hapmap]
rs10504158	1.00[CEU][hapmap]
rs11985729	0.83[ASN][1000 genomes]
rs1384797	1.00[CEU][hapmap]
rs1483538	1.00[CEU][hapmap]
rs1483539	1.00[CEU][hapmap]
rs1483540	1.00[CEU][hapmap]
rs1483542	1.00[CEU][hapmap]
rs1842983	1.00[CEU][hapmap]
rs1842984	1.00[CEU][hapmap]
rs2306584	0.84[EUR][1000 genomes]
rs2306585	0.80[ASN][1000 genomes]
rs4737974	0.83[GIH][hapmap];0.82[YRI][hapmap]
rs4738025	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4738027	0.82[YRI][hapmap]
rs56956173	0.85[AFR][1000 genomes]
rs60696924	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60819522	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61194604	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61433056	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6473893	0.81[GIH][hapmap]
rs6473894	1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6984257	0.82[YRI][hapmap]
rs6994332	0.81[ASN][1000 genomes]
rs6997050	1.00[CEU][hapmap]
rs6998532	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7016171	0.81[ASN][1000 genomes]
rs7017291	1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73680321	0.81[AFR][1000 genomes]
rs73680325	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7827611	1.00[CEU][hapmap]
rs7830107	1.00[TSI][hapmap]
rs7831399	1.00[CEU][hapmap]
rs7846259	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9643820	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54710200-54755000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:54724800-54754800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:54738800-54754800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:54738800-54755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:54741800-54754800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:54744200-54754800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:54750400-54754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:54750600-54755000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr8:54751600-54754400	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr8:54752000-54754800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr8:54752400-54754600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr8:54752400-54755000	Weak transcription	Left Ventricle	heart
13	chr8:54752600-54755000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr8:54752800-54755000	Weak transcription	Aorta	Aorta
15	chr8:54753200-54754400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr8:54753200-54754600	Enhancers	Liver	Liver
17	chr8:54753400-54754400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr8:54753400-54754400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr8:54753400-54754400	Enhancers	Fetal Brain Female	brain
20	chr8:54753400-54755000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr8:54753400-54755200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:54753400-54756600	Active TSS	Brain Anterior Caudate	brain
23	chr8:54753600-54754400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:54753600-54754400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr8:54753600-54754400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:54753600-54754400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:54753600-54754400	Enhancers	Placenta	Placenta
28	chr8:54753600-54754400	Enhancers	Small Intestine	intestine
29	chr8:54753600-54754400	Flanking Active TSS	HMEC	breast
30	chr8:54753600-54754600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr8:54753600-54754600	Enhancers	Adipose Nuclei	Adipose
32	chr8:54753600-54754600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr8:54753600-54754800	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr8:54753600-54754800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr8:54753600-54754800	Enhancers	Stomach Mucosa	stomach
36	chr8:54753600-54755000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr8:54753600-54755400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:54753600-54755400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr8:54753600-54756600	Active TSS	NHLF	lung
40	chr8:54753800-54754400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr8:54753800-54754400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:54753800-54754400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr8:54753800-54754400	Genic enhancers	Fetal Thymus	thymus
44	chr8:54753800-54754400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr8:54753800-54754400	Genic enhancers	HSMM	muscle
46	chr8:54753800-54754400	Flanking Active TSS	HSMMtube	muscle
47	chr8:54753800-54754600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr8:54753800-54754600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr8:54753800-54754800	Enhancers	Primary B cells from cord blood	blood
50	chr8:54753800-54754800	Enhancers	Brain Substantia Nigra	brain

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