Variant report

Variant	rs2803196
Chromosome Location	chr6:80234343-80234344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:80233865..80235621-chr6:80253239..80255596,2	K562	blood:
2	chr6:80227058..80229732-chr6:80232396..80234486,2	MCF-7	breast:
3	chr6:80234104..80236785-chr6:80239338..80241775,2	K562	blood:
4	chr6:80233273..80237296-chr6:80243465..80250344,8	K562	blood:
5	chr6:80232386..80237378-chr6:80253283..80257767,7	K562	blood:
6	chr6:80233762..80237001-chr6:80242844..80245026,3	K562	blood:

Variant related genes	Relation type
ENSG00000135338	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1385533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1385535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1485368	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1847499	1.00[AMR][1000 genomes]
rs1875846	1.00[EUR][1000 genomes]
rs2575199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655664	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655667	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2655702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2803187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2803198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2814374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2814387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2814389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56010310	1.00[EUR][1000 genomes]
rs57177286	1.00[EUR][1000 genomes]
rs9448702	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv1798451	chr6:80222511-80234343	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2803196	CD4	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80179800-80235000	Weak transcription	HSMMtube	muscle
2	chr6:80190200-80234400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:80195400-80235000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:80198400-80235000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:80199000-80235000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:80207600-80246000	Weak transcription	Ovary	ovary
7	chr6:80209000-80235000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:80214400-80235000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:80214600-80246000	Weak transcription	Fetal Stomach	stomach
10	chr6:80216000-80236800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:80216400-80235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:80216400-80235000	Weak transcription	NH-A	brain
13	chr6:80217600-80235000	Weak transcription	Pancreas	Pancrea
14	chr6:80217800-80246000	Weak transcription	Aorta	Aorta
15	chr6:80218200-80244000	Weak transcription	Fetal Brain Female	brain
16	chr6:80219000-80235400	Weak transcription	Fetal Heart	heart
17	chr6:80221400-80235600	Weak transcription	Fetal Kidney	kidney
18	chr6:80221800-80234400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:80222400-80235200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:80223400-80234800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:80223400-80240400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:80225800-80235000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:80227400-80234800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:80228000-80241800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:80229000-80234800	Weak transcription	HSMM	muscle
26	chr6:80232600-80236000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:80233400-80234800	Enhancers	HepG2	liver
28	chr6:80233600-80234400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:80233800-80234800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:80233800-80235000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:80233800-80236200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:80234000-80235000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:80234000-80235000	Enhancers	HMEC	breast
34	chr6:80234000-80235000	Enhancers	K562	blood
35	chr6:80234200-80235000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:80234200-80236000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:80234200-80243000	Weak transcription	Fetal Lung	lung
38	chr6:80234200-80246000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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