Variant report

Variant	rs230644
Chromosome Location	chr21:44917183-44917184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:44903994..44910512-chr21:44911444..44917945,16	MCF-7	breast:
2	chr21:44841823..44851058-chr21:44912330..44925700,37	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1003280	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1073522	0.83[ASN][1000 genomes]
rs11089020	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1122873	0.81[ASN][1000 genomes]
rs11701673	0.80[EUR][1000 genomes]
rs12626757	0.82[ASN][1000 genomes]
rs1378079	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1378080	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs141521	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1454650	0.82[ASN][1000 genomes]
rs1454651	0.82[ASN][1000 genomes]
rs1584917	0.81[ASN][1000 genomes]
rs1584918	0.81[ASN][1000 genomes]
rs162343	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162344	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162345	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162366	0.87[ASN][1000 genomes]
rs162367	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162368	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs162369	0.88[ASN][1000 genomes]
rs162371	0.86[ASN][1000 genomes]
rs162372	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162373	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162374	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162375	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162376	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162377	0.90[ASN][1000 genomes]
rs162378	0.91[ASN][1000 genomes]
rs162379	0.86[EUR][1000 genomes]
rs162380	0.92[ASN][1000 genomes]
rs162381	0.94[ASN][1000 genomes]
rs162388	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162389	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs162390	0.87[ASN][1000 genomes]
rs162391	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162393	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162394	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162395	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162398	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162399	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162400	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162401	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs162402	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162403	0.85[ASN][1000 genomes]
rs162404	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs167930	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs189094	0.88[ASN][1000 genomes]
rs229357	0.82[ASN][1000 genomes]
rs230640	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230641	0.87[EUR][1000 genomes]
rs230642	0.93[ASN][1000 genomes]
rs230643	0.93[ASN][1000 genomes]
rs230645	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs230646	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230647	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2329442	0.81[ASN][1000 genomes]
rs2838316	0.82[ASN][1000 genomes]
rs2838317	0.82[ASN][1000 genomes]
rs2838319	0.82[ASN][1000 genomes]
rs2838321	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838322	0.82[ASN][1000 genomes]
rs2838323	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838324	0.82[ASN][1000 genomes]
rs2838328	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2838329	0.83[ASN][1000 genomes]
rs2838330	0.83[ASN][1000 genomes]
rs2838331	0.83[ASN][1000 genomes]
rs28840140	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3788062	0.82[ASN][1000 genomes]
rs463738	0.93[ASN][1000 genomes]
rs4818843	0.82[ASN][1000 genomes]
rs4818850	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818856	0.81[ASN][1000 genomes]
rs4819264	0.81[ASN][1000 genomes]
rs4819270	0.83[ASN][1000 genomes]
rs4997353	0.86[EUR][1000 genomes]
rs6518301	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6518302	0.83[ASN][1000 genomes]
rs6518309	0.81[ASN][1000 genomes]
rs7276215	0.80[ASN][1000 genomes]
rs7279958	0.83[ASN][1000 genomes]
rs7282933	0.81[ASN][1000 genomes]
rs86138	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs86139	0.88[ASN][1000 genomes]
rs91424	0.94[ASN][1000 genomes]
rs9976441	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9978811	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9981291	0.83[ASN][1000 genomes]
rs9981790	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9983763	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
5	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
6	nsv913847	chr21:44792003-44931821	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
7	nsv913849	chr21:44817248-44925334	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv913852	chr21:44829087-44925334	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
9	nsv913860	chr21:44831981-44925334	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv913867	chr21:44835508-44925334	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv913868	chr21:44835508-44954522	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv913872	chr21:44860542-44925334	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	esv1839560	chr21:44864079-44973184	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
14	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
15	nsv587689	chr21:44884252-44986050	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
16	nsv1061369	chr21:44886596-44931388	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv544468	chr21:44886596-44931388	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1059264	chr21:44895863-44944515	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
19	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44912800-44918400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr21:44914000-44918000	Weak transcription	Right Atrium	heart
3	chr21:44914600-44917600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr21:44914600-44918000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr21:44914600-44918000	Weak transcription	Adipose Nuclei	Adipose
6	chr21:44914600-44921800	Weak transcription	Colonic Mucosa	Colon
7	chr21:44914600-44921800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr21:44914600-44922200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:44914800-44918200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:44914800-44922000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr21:44915000-44918000	Weak transcription	Brain Anterior Caudate	brain
12	chr21:44915000-44918200	Weak transcription	Liver	Liver
13	chr21:44915000-44918600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr21:44915000-44919600	Weak transcription	Esophagus	oesophagus
15	chr21:44915000-44921800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:44915000-44921800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr21:44915000-44922000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr21:44915000-44922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:44915000-44922400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr21:44915200-44917400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:44915200-44917400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr21:44915200-44917400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr21:44915200-44917400	Weak transcription	NHLF	lung
24	chr21:44915200-44917600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr21:44915200-44917600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr21:44915200-44917800	Weak transcription	Lung	lung
27	chr21:44915200-44917800	Weak transcription	Right Ventricle	heart
28	chr21:44915200-44917800	Weak transcription	HUVEC	blood vessel
29	chr21:44915200-44918200	Weak transcription	Brain Angular Gyrus	brain
30	chr21:44915400-44917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr21:44915400-44917800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr21:44915400-44917800	Enhancers	Hela-S3	cervix
33	chr21:44915400-44918000	Weak transcription	Gastric	stomach
34	chr21:44915400-44922200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr21:44915600-44917800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr21:44915600-44917800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr21:44915600-44918000	Weak transcription	Psoas Muscle	Psoas
38	chr21:44915600-44918200	Weak transcription	Stomach Mucosa	stomach
39	chr21:44915600-44918400	Enhancers	HSMM	muscle
40	chr21:44915800-44917200	Weak transcription	NHEK	skin
41	chr21:44915800-44917400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr21:44915800-44917600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr21:44915800-44917800	Weak transcription	Placenta	Placenta
44	chr21:44916000-44917200	Weak transcription	A549	lung
45	chr21:44916000-44917200	Enhancers	HSMMtube	muscle
46	chr21:44916000-44917400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr21:44916000-44917400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr21:44916200-44917200	Weak transcription	Osteobl	bone
49	chr21:44916400-44917800	Weak transcription	HepG2	liver
50	chr21:44916800-44920600	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links