Variant report

Variant	rs28844358
Chromosome Location	chr7:124562695-124562696
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:124560803..124563318-chr7:124567698..124570085,3	K562	blood:
2	chr7:124546480..124548936-chr7:124561383..124564382,2	K562	blood:
3	chr7:124537777..124539651-chr7:124561497..124564089,2	K562	blood:

Variant related genes	Relation type
ENSG00000224897	Chromatin interaction
ENSG00000128513	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10224463	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10225552	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10226033	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10228201	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10230610	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10233385	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10233596	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10240673	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241173	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10244817	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10246424	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10249722	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253613	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10264060	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10265763	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10271646	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281582	0.86[ASN][1000 genomes]
rs10464529	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12111865	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1541416	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541418	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17246404	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2107939	0.89[ASN][1000 genomes]
rs2239532	0.81[ASN][1000 genomes]
rs2286175	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2402751	0.89[ASN][1000 genomes]
rs2402752	0.91[ASN][1000 genomes]
rs28523990	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28622327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638102	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28728448	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34986416	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36045816	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3925331	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4473974	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4532534	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55964341	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56313563	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321835	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56356267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56387611	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58618031	0.81[EUR][1000 genomes]
rs59294613	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59670428	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492217	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66513837	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66526112	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66665074	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66922607	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67084428	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67146030	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67552763	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67585224	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67870530	0.84[EUR][1000 genomes]
rs67939974	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68007199	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68091803	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943653	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952721	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6971909	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720613	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720614	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs722560	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs727505	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7777947	0.91[ASN][1000 genomes]
rs7790856	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7791430	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7795943	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7801661	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7806680	0.91[ASN][1000 genomes]
rs9655845	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989177	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv889135	chr7:124462081-124584834	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv464707	chr7:124486980-124572288	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv608341	chr7:124486980-124572288	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv889137	chr7:124513770-124584834	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv889138	chr7:124518766-124584834	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv608342	chr7:124549573-124600505	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124462200-124568200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr7:124466600-124563400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:124498200-124568800	Weak transcription	Brain Anterior Caudate	brain
4	chr7:124522800-124568400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:124527600-124569000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:124527600-124569000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:124528000-124567400	Weak transcription	HepG2	liver
8	chr7:124529800-124564400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:124530000-124569000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:124532000-124569000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr7:124532600-124568400	Weak transcription	NHDF-Ad	bronchial
12	chr7:124532600-124568800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:124532600-124569000	Weak transcription	HSMM	muscle
14	chr7:124532800-124568400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:124532800-124569000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:124533200-124562800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:124535800-124563000	Weak transcription	Primary T cells from cord blood	blood
18	chr7:124537800-124566000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:124538000-124569200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:124541000-124568600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:124541000-124569000	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:124541400-124568800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:124541400-124568800	Weak transcription	Fetal Intestine Small	intestine
24	chr7:124541400-124569000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:124541400-124569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:124541400-124569000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:124541400-124569400	Weak transcription	Lung	lung
28	chr7:124541600-124565800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr7:124541600-124569200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:124544600-124564400	Weak transcription	Hela-S3	cervix
31	chr7:124548400-124569000	Weak transcription	NH-A	brain
32	chr7:124550200-124569200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:124550600-124566000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:124550600-124568800	Weak transcription	Fetal Intestine Large	intestine
35	chr7:124550800-124569000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr7:124551000-124569000	Weak transcription	HSMMtube	muscle
37	chr7:124551400-124568800	Weak transcription	Fetal Kidney	kidney
38	chr7:124551800-124568800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:124552400-124569000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:124553200-124568800	Weak transcription	Fetal Thymus	thymus
41	chr7:124553400-124566800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:124553400-124568800	Weak transcription	HMEC	breast
43	chr7:124553800-124568400	Weak transcription	Fetal Lung	lung
44	chr7:124554600-124566400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr7:124554600-124568600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:124555400-124569000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:124555600-124566200	Weak transcription	K562	blood
48	chr7:124555600-124566800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:124555600-124566800	Weak transcription	Liver	Liver
50	chr7:124555600-124568400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links