Variant report

Variant	rs6430299
Chromosome Location	chr2:148942537-148942538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10084287	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1037300	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10427294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1227474	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1227477	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1227478	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1227480	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1227483	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12623429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1375860	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1530757	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16828211	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16828213	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2603601	0.82[AFR][1000 genomes]
rs2603605	0.83[AFR][1000 genomes]
rs2627024	0.82[AFR][1000 genomes]
rs4312431	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4383275	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972271	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4972335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56986186	0.84[AFR][1000 genomes]
rs6713738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6728673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6739781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73964199	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7574172	0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv997674	chr2:148862630-148995570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1007998	chr2:148866051-148995570	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv915953	chr2:148934787-148977722	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148913000-148977600	Weak transcription	Aorta	Aorta
2	chr2:148919800-148945800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:148924400-148946400	Weak transcription	HSMMtube	muscle
4	chr2:148924600-148946800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:148925200-148959000	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:148927200-148942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:148928200-148945400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:148928400-148943800	Weak transcription	Fetal Brain Female	brain
9	chr2:148928400-148944600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:148928600-148993600	Weak transcription	HSMM	muscle
11	chr2:148928800-148945600	Weak transcription	Primary T cells from cord blood	blood
12	chr2:148929600-148944800	Weak transcription	Osteobl	bone
13	chr2:148929800-148944400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:148929800-148960800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:148930600-148946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:148930800-148948200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:148931000-148942600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:148931000-148960600	Weak transcription	Spleen	Spleen
19	chr2:148931200-148944200	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:148931200-148948400	Weak transcription	Pancreas	Pancrea
21	chr2:148931200-148958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:148931200-148993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:148933800-148953400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:148934200-148943400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:148934400-148943600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:148934600-148943800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:148934600-148943800	Weak transcription	Liver	Liver
28	chr2:148935400-148944400	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:148935400-148946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:148935600-148943800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:148935600-148945000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:148935600-148945400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:148935600-148946000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:148935600-148946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:148935800-148945400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:148936000-148944200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:148936400-148945000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:148936800-148946000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:148937400-148946600	Weak transcription	Adipose Nuclei	Adipose
40	chr2:148937800-148945200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:148938400-148958600	Weak transcription	Fetal Intestine Small	intestine
42	chr2:148938400-148969200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:148938600-148944600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:148938600-148947400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:148939000-148945400	Weak transcription	Fetal Thymus	thymus
46	chr2:148939000-148946600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:148939000-148958600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:148939200-148944000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:148940400-148943000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:148940400-148943800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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