Variant report

Variant	rs6550829
Chromosome Location	chr3:24038687-24038688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23986774..23989420-chr3:24037781..24039507,2	K562	blood:
2	chr3:23986774..23988975-chr3:24037159..24039281,2	K562	blood:
3	chr3:24030711..24032570-chr3:24036287..24038939,2	K562	blood:
4	chr3:24033672..24036269-chr3:24038559..24040609,2	K562	blood:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13095392	0.86[CHB][hapmap]
rs4241517	0.84[ASW][hapmap];0.82[CHB][hapmap]
rs4321479	0.82[CHB][hapmap]
rs4589882	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs4858095	0.86[CHB][hapmap]
rs4858098	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs4858567	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs5023610	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs6550823	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs6550827	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6550828	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6778783	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793391	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6794922	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs6807856	0.86[MKK][hapmap]
rs7371944	0.82[YRI][hapmap]
rs9310725	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv834639	chr3:24037113-24233925	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24019600-24040800	Weak transcription	NHLF	lung
2	chr3:24030800-24040400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:24033600-24039000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:24033600-24040600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:24033800-24040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:24034200-24039000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:24034600-24040400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:24035200-24040600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:24035800-24040400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:24035800-24040600	Weak transcription	Brain Angular Gyrus	brain
11	chr3:24036000-24040400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:24036000-24040400	Weak transcription	HSMMtube	muscle
13	chr3:24036000-24040400	Weak transcription	NHDF-Ad	bronchial
14	chr3:24036000-24040600	Weak transcription	Brain Germinal Matrix	brain
15	chr3:24036000-24040600	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:24036000-24040600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:24036000-24040600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:24036000-24040800	Weak transcription	Ovary	ovary
19	chr3:24036000-24053400	Weak transcription	Psoas Muscle	Psoas
20	chr3:24036200-24040400	Weak transcription	Adipose Nuclei	Adipose
21	chr3:24036200-24040600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:24036200-24040600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:24036200-24040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:24036200-24040600	Weak transcription	Fetal Kidney	kidney
25	chr3:24036200-24040600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:24036200-24040600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:24036200-24040800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:24036400-24040400	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:24036400-24040800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:24036400-24043600	Weak transcription	Aorta	Aorta
31	chr3:24037200-24038800	Enhancers	Fetal Lung	lung
32	chr3:24038000-24039000	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:24038000-24040800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:24038600-24040400	Weak transcription	Fetal Stomach	stomach

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