Variant report

Variant	rs28664200
Chromosome Location	chr4:102251501-102251502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10017730	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1031033	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1031034	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1031035	0.96[EUR][1000 genomes]
rs10433980	0.80[EUR][1000 genomes]
rs10433981	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10433982	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11097747	0.80[AMR][1000 genomes]
rs12499349	0.80[AMR][1000 genomes]
rs13109704	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13135111	0.80[AMR][1000 genomes]
rs13135270	0.80[AMR][1000 genomes]
rs13135441	0.80[EUR][1000 genomes]
rs13148622	0.80[AMR][1000 genomes]
rs13148645	0.80[AMR][1000 genomes]
rs1348161	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1476159	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1530259	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1596061	0.80[AMR][1000 genomes]
rs1822168	0.80[EUR][1000 genomes]
rs1822169	0.80[EUR][1000 genomes]
rs2044043	0.94[EUR][1000 genomes]
rs2119593	0.80[AMR][1000 genomes]
rs2119596	0.80[AMR][1000 genomes]
rs2583385	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2583386	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2583387	0.81[EUR][1000 genomes]
rs2583389	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2583391	0.95[EUR][1000 genomes]
rs2583392	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583394	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583395	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583397	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583398	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583399	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850326	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2850328	0.89[EUR][1000 genomes]
rs2850329	0.90[EUR][1000 genomes]
rs2850330	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850331	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850333	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2850334	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2850355	0.81[ASN][1000 genomes]
rs2850356	0.81[ASN][1000 genomes]
rs2850358	0.83[ASN][1000 genomes]
rs2850360	0.86[ASN][1000 genomes]
rs2850366	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850367	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850368	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850369	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850371	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850372	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4574415	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4698957	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4699209	0.81[EUR][1000 genomes]
rs4699210	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4699211	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4699212	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4699213	0.80[AMR][1000 genomes]
rs4699214	0.80[EUR][1000 genomes]
rs6532928	0.80[EUR][1000 genomes]
rs6532929	0.80[AMR][1000 genomes]
rs6532930	0.80[AMR][1000 genomes]
rs6816400	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6824603	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6845368	0.82[EUR][1000 genomes]
rs6846097	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6852377	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6856370	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7668224	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7670594	0.80[AMR][1000 genomes]
rs7670922	0.80[AMR][1000 genomes]
rs7677595	0.80[AMR][1000 genomes]
rs7687487	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs920560	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28664200	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102243200-102251600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:102243200-102251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:102243400-102252000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:102243400-102256000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:102243600-102251800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:102243600-102256800	Weak transcription	Aorta	Aorta
7	chr4:102244000-102258000	Weak transcription	Brain Angular Gyrus	brain
8	chr4:102245400-102251600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:102245600-102251800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:102245600-102252800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:102245600-102255000	Weak transcription	Ovary	ovary
12	chr4:102245800-102252000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:102247400-102251600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:102247800-102251800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:102248000-102252000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:102248000-102252200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:102249200-102252200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:102249600-102266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:102249800-102251800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:102249800-102252000	Enhancers	Primary T cells from cord blood	blood
21	chr4:102249800-102252200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:102249800-102252400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:102249800-102256000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:102250000-102253200	Weak transcription	Primary B cells from cord blood	blood
25	chr4:102250200-102258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:102250200-102265200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:102250400-102252000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:102250400-102265800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:102250600-102252400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr4:102250600-102255000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:102250600-102255800	Weak transcription	GM12878-XiMat	blood
32	chr4:102250600-102266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:102250800-102255000	Weak transcription	Gastric	stomach
34	chr4:102251000-102252000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:102251000-102252200	Weak transcription	Psoas Muscle	Psoas
36	chr4:102251000-102252600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:102251000-102252600	Enhancers	Colon Smooth Muscle	Colon
38	chr4:102251000-102256200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:102251000-102256200	Weak transcription	Liver	Liver
40	chr4:102251000-102256200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:102251000-102256400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:102251000-102256400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr4:102251000-102258200	Weak transcription	Dnd41	blood
44	chr4:102251000-102260200	Weak transcription	Brain Anterior Caudate	brain
45	chr4:102251200-102255800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:102251200-102255800	Weak transcription	Small Intestine	intestine
47	chr4:102251200-102256200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:102251200-102258000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:102251200-102259600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:102251200-102265800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links