Variant report

Variant	rs6828824
Chromosome Location	chr4:166250224-166250225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:166127386..166130072-chr4:166247171..166250406,6	MCF-7	breast:
2	chr4:166127276..166130366-chr4:166247405..166250443,3	K562	blood:
3	chr4:166126308..166130366-chr4:166247405..166251145,5	K562	blood:
4	chr4:166249129..166252121-chr4:166265324..166266921,2	K562	blood:

Variant related genes	Relation type
ENSG00000109466	Chromatin interaction
ENSG00000170088	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10009994	0.96[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10015240	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11726531	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs13353543	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16999615	0.85[MEX][hapmap]
rs17842697	0.85[MEX][hapmap]
rs17842699	0.85[MEX][hapmap]
rs28678193	0.92[EUR][1000 genomes]
rs28678592	0.89[CEU][hapmap]
rs3756015	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4588420	0.89[CEU][hapmap]
rs57720293	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60759634	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6536903	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830714	0.85[MEX][hapmap]
rs7662569	0.82[CEU][hapmap]
rs7685245	0.85[MEX][hapmap]
rs7698056	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9685465	0.87[JPT][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	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 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	chr4:166247000-166251600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:166247400-166250400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:166247600-166250400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr4:166247600-166250400	Active TSS	Brain Substantia Nigra	brain
5	chr4:166247600-166250400	Active TSS	Right Atrium	heart
6	chr4:166247600-166251400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:166247600-166251600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:166247600-166251800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:166247800-166250400	Active TSS	Aorta	Aorta
10	chr4:166247800-166250400	Active TSS	Fetal Muscle Trunk	muscle
11	chr4:166247800-166250400	Active TSS	Ovary	ovary
12	chr4:166247800-166250400	Active TSS	HSMM	muscle
13	chr4:166247800-166250600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr4:166247800-166250800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr4:166247800-166251000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr4:166247800-166251000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:166247800-166251000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:166247800-166251000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:166247800-166251000	Active TSS	Fetal Intestine Small	intestine
20	chr4:166247800-166251200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr4:166247800-166251200	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr4:166247800-166251400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr4:166247800-166251400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:166247800-166251400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:166247800-166251400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr4:166247800-166251400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:166247800-166251400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:166247800-166251400	Active TSS	GM12878-XiMat	blood
29	chr4:166247800-166251400	Active TSS	NHDF-Ad	bronchial
30	chr4:166247800-166251600	Active TSS	Fetal Intestine Large	intestine
31	chr4:166247800-166251800	Active TSS	HSMMtube	muscle
32	chr4:166247800-166253600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:166248000-166250400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:166248000-166250400	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr4:166248000-166250400	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr4:166248000-166250600	Active TSS	Colonic Mucosa	Colon
37	chr4:166248000-166251000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:166248000-166251000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:166248000-166251000	Active TSS	NHEK	skin
40	chr4:166248000-166251000	Active TSS	NHLF	lung
41	chr4:166248000-166251200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:166248000-166251200	Active TSS	Esophagus	oesophagus
43	chr4:166248000-166251200	Active TSS	HMEC	breast
44	chr4:166248000-166251400	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr4:166248000-166252000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:166248000-166253200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:166248000-166253600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:166248200-166250600	Bivalent/Poised TSS	HepG2	liver
49	chr4:166249000-166250400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:166249000-166250800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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