Variant report

Variant	rs6823351
Chromosome Location	chr4:48561450-48561451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10029425	1.00[AMR][1000 genomes]
rs10034207	1.00[AMR][1000 genomes]
rs10049760	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10755182	1.00[AMR][1000 genomes]
rs10805171	1.00[AMR][1000 genomes]
rs10805172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10938535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10938538	1.00[AMR][1000 genomes]
rs10938539	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10938541	1.00[AMR][1000 genomes]
rs12500224	1.00[AMR][1000 genomes]
rs12500244	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12500570	0.85[AFR][1000 genomes]
rs12507546	1.00[AMR][1000 genomes]
rs13125379	1.00[AMR][1000 genomes]
rs1474072	1.00[AMR][1000 genomes]
rs1517673	1.00[AMR][1000 genomes]
rs1517676	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1517677	1.00[AMR][1000 genomes]
rs1533511	1.00[AMR][1000 genomes]
rs1554257	1.00[AMR][1000 genomes]
rs1616561	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702796	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702799	1.00[AMR][1000 genomes]
rs1712771	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1949422	1.00[AMR][1000 genomes]
rs2138866	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2138867	1.00[AMR][1000 genomes]
rs28371079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28558226	0.90[AFR][1000 genomes]
rs2883410	1.00[AMR][1000 genomes]
rs2940319	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4235155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4235157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4330326	1.00[AMR][1000 genomes]
rs4558842	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694896	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694898	1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695386	1.00[AMR][1000 genomes]
rs4695390	1.00[AMR][1000 genomes]
rs4695402	1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs4998005	1.00[AMR][1000 genomes]
rs6447642	1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	1.00[AMR][1000 genomes]
rs6447657	1.00[AMR][1000 genomes]
rs6821456	1.00[AMR][1000 genomes]
rs6827481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6828500	1.00[AMR][1000 genomes]
rs6835757	1.00[AMR][1000 genomes]
rs6844088	1.00[AMR][1000 genomes]
rs6846797	1.00[AMR][1000 genomes]
rs6848222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6848417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6849798	1.00[AMR][1000 genomes]
rs6853876	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs707720	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7434721	1.00[AMR][1000 genomes]
rs7664507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689662	1.00[AMR][1000 genomes]
rs7692480	1.00[AMR][1000 genomes]
rs7698064	1.00[AMR][1000 genomes]
rs776581	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776583	1.00[AMR][1000 genomes]
rs776587	1.00[AMR][1000 genomes]
rs776589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776595	1.00[AMR][1000 genomes]
rs776603	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs938791	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994214	1.00[AMR][1000 genomes]
rs9997932	1.00[AMR][1000 genomes]
rs9998178	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48499000-48578800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:48499600-48581400	Strong transcription	Dnd41	blood
5	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48501400-48578600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:48504400-48575400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48505200-48575400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:48507200-48564000	Strong transcription	Fetal Thymus	thymus
10	chr4:48507600-48568600	Strong transcription	Primary T cells from cord blood	blood
11	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
12	chr4:48519400-48566200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48522600-48563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:48540600-48580400	Strong transcription	Fetal Intestine Large	intestine
17	chr4:48540800-48576000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:48541000-48580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:48541000-48587800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:48541200-48566600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:48541200-48567000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr4:48541400-48566200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:48541400-48581200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:48541600-48568800	Strong transcription	Placenta	Placenta
26	chr4:48541600-48581400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:48541800-48579800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr4:48542400-48564000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:48542400-48564000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:48542400-48568200	Strong transcription	Brain Substantia Nigra	brain
31	chr4:48542800-48604400	Weak transcription	A549	lung
32	chr4:48544400-48566000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:48546000-48571800	Weak transcription	Psoas Muscle	Psoas
35	chr4:48546400-48596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:48546600-48578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:48547400-48578800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:48547400-48593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:48549400-48563200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:48549400-48565800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:48549400-48575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:48549600-48564600	Strong transcription	Fetal Muscle Leg	muscle
43	chr4:48549600-48566400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:48549600-48569200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:48549600-48569400	Strong transcription	Liver	Liver
46	chr4:48549600-48570200	Strong transcription	Fetal Lung	lung
47	chr4:48550000-48567800	Strong transcription	HUVEC	blood vessel
48	chr4:48550200-48568400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:48550800-48564600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr4:48551000-48563600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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