Variant report

Variant	rs2844649
Chromosome Location	chr6:30904272-30904273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30902336..30907569-chr6:30907613..30911595,7	K562	blood:
2	chr6:30900647..30902289-chr6:30902936..30905362,2	MCF-7	breast:
3	chr6:30849409..30852184-chr6:30904087..30906544,3	MCF-7	breast:
4	chr6:30901740..30904326-chr6:30904542..30906468,2	K562	blood:

Variant related genes	Relation type
ENSG00000168631	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1264295	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517451	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844650	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844701	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131922	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3132572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2844649	HCG22	cis	lymphoblastoid	seeQTL
rs2844649	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30894800-30905000	Weak transcription	Right Ventricle	heart
2	chr6:30896000-30904400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:30896600-30905800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:30897000-30905600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:30897000-30905800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:30897000-30909800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:30897200-30905600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:30899400-30904600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:30900200-30906800	Enhancers	Stomach Mucosa	stomach
10	chr6:30901000-30905000	Weak transcription	Esophagus	oesophagus
11	chr6:30902000-30906200	Weak transcription	Pancreas	Pancrea
12	chr6:30903200-30906000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:30903200-30906200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:30903200-30906600	Weak transcription	HMEC	breast
15	chr6:30904000-30905000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:30904000-30905200	Active TSS	Lung	lung
17	chr6:30904000-30905400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:30904200-30904800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr6:30904200-30910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:30904200-30910200	Weak transcription	Placenta Amnion	Placenta Amnion

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