Variant report

Variant	rs6550824
Chromosome Location	chr3:24022671-24022672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23958659..23961020-chr3:24021622..24024161,2	K562	blood:
2	chr3:24014593..24017438-chr3:24020273..24022984,2	K562	blood:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11717862	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091509	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13095392	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131403	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241514	0.81[EUR][1000 genomes]
rs4241515	0.92[AFR][1000 genomes]
rs4241517	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4241520	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4320034	0.84[AFR][1000 genomes]
rs4321479	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4589882	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619734	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858095	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858098	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858565	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858567	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253379	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419846	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550815	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6550819	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6550823	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6778783	0.88[EUR][1000 genomes]
rs6779476	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6790557	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793391	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6794922	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7371944	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7431301	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9310725	0.86[EUR][1000 genomes]
rs9879378	0.85[EUR][1000 genomes]
rs9882735	0.97[EUR][1000 genomes]

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	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

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:24004000-24023400	Weak transcription	Gastric	stomach
4	chr3:24004000-24023800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:24005600-24032800	Weak transcription	NH-A	brain
6	chr3:24007800-24023200	Weak transcription	Colonic Mucosa	Colon
7	chr3:24010200-24023800	Weak transcription	Psoas Muscle	Psoas
8	chr3:24010200-24028800	Weak transcription	HUVEC	blood vessel
9	chr3:24010400-24024000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:24018200-24022800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:24018200-24022800	Weak transcription	Dnd41	blood
12	chr3:24018200-24023600	Weak transcription	Lung	lung
13	chr3:24018200-24024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:24018200-24024400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:24018200-24024600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:24018200-24033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:24018400-24022800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:24018400-24024800	Weak transcription	GM12878-XiMat	blood
19	chr3:24018400-24032200	Weak transcription	Fetal Brain Female	brain
20	chr3:24018400-24032400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:24019200-24024000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:24019400-24022800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:24019400-24024000	Weak transcription	Ovary	ovary
24	chr3:24019400-24024200	Weak transcription	Brain Substantia Nigra	brain
25	chr3:24019400-24025000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:24019400-24025200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:24019400-24032800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:24019400-24032800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:24019400-24032800	Weak transcription	Primary T cells from cord blood	blood
30	chr3:24019400-24032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:24019400-24033200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:24019400-24035400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:24019600-24022800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:24019600-24023200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:24019600-24024800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:24019600-24025000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:24019600-24025200	Weak transcription	Primary B cells from cord blood	blood
38	chr3:24019600-24025200	Weak transcription	Hela-S3	cervix
39	chr3:24019600-24027600	Weak transcription	Fetal Brain Male	brain
40	chr3:24019600-24028600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:24019600-24040800	Weak transcription	NHLF	lung
42	chr3:24019800-24022800	Weak transcription	Brain Anterior Caudate	brain
43	chr3:24019800-24023200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:24019800-24024400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:24019800-24024800	Weak transcription	HepG2	liver
46	chr3:24020200-24022800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:24020200-24032800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:24020600-24022800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:24020600-24023800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:24020800-24022800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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