Variant report

Variant	rs6848200
Chromosome Location	chr4:53730181-53730182
allele	A/G
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	POLR2A	chr4:53730130-53730330	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr4:53729310-53731670	SK-N-SH	brain:	n/a	chr4:53730198-53730206
3	MXI1	chr4:53726951-53732052	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53586938..53589965-chr4:53727574..53731676,3	MCF-7	breast:

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000248375	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10517269	0.89[AMR][1000 genomes]
rs11938159	0.87[AMR][1000 genomes]
rs11939448	0.85[AMR][1000 genomes]
rs17082074	0.84[ASN][1000 genomes]
rs17082087	0.80[AMR][1000 genomes]
rs17082091	0.85[AMR][1000 genomes]
rs2200225	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3811781	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41279517	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58461944	0.80[AMR][1000 genomes]
rs58577680	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59042894	0.85[AMR][1000 genomes]
rs6554054	0.87[AMR][1000 genomes]
rs6554057	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817433	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6818178	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6838718	0.87[AMR][1000 genomes]
rs73814868	0.89[AMR][1000 genomes]
rs73814875	0.95[ASN][1000 genomes]
rs73814883	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814886	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7655781	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7663419	0.85[AMR][1000 genomes]
rs7670068	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7685816	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7688141	0.87[AMR][1000 genomes]
rs7693568	0.85[AMR][1000 genomes]
rs7699960	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs881744	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53727800-53730800	Active TSS	Aorta	Aorta
2	chr4:53727800-53731800	Active TSS	Fetal Kidney	kidney
3	chr4:53728000-53730200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:53728000-53730400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:53728600-53730200	Active TSS	Right Atrium	heart
6	chr4:53728800-53731000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr4:53728800-53738400	Weak transcription	Small Intestine	intestine
8	chr4:53729200-53730200	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
9	chr4:53729200-53731800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:53729200-53732000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
11	chr4:53729200-53734200	Weak transcription	Psoas Muscle	Psoas
12	chr4:53729200-53734400	Weak transcription	HSMMtube	muscle
13	chr4:53729200-53735200	Weak transcription	Colonic Mucosa	Colon
14	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
15	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
16	chr4:53729400-53730600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:53729400-53730600	Weak transcription	Gastric	stomach
18	chr4:53729400-53730800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:53729400-53731000	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:53729400-53731200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:53729400-53731400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:53729400-53731400	Weak transcription	Left Ventricle	heart
23	chr4:53729400-53731400	Weak transcription	Pancreas	Pancrea
24	chr4:53729400-53731400	Weak transcription	Right Ventricle	heart
25	chr4:53729400-53731600	Weak transcription	Lung	lung
26	chr4:53729400-53732000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
27	chr4:53729400-53732200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
28	chr4:53729400-53734000	Weak transcription	Brain Anterior Caudate	brain
29	chr4:53729400-53738600	Weak transcription	HMEC	breast
30	chr4:53729400-53739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
33	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:53729600-53730600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:53729600-53730800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
36	chr4:53729600-53730800	Weak transcription	Spleen	Spleen
37	chr4:53729600-53731200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
38	chr4:53729600-53731200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:53729600-53731200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:53729600-53731400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:53729600-53731600	Enhancers	Stomach Mucosa	stomach
42	chr4:53729600-53731600	Weak transcription	NHLF	lung
43	chr4:53729600-53732800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:53729600-53733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:53729600-53733800	Weak transcription	NHEK	skin
46	chr4:53729600-53734000	Weak transcription	Brain Angular Gyrus	brain
47	chr4:53729600-53735200	Weak transcription	NHDF-Ad	bronchial
48	chr4:53729600-53739400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:53729600-53739600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:53729600-53742200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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