Variant report

Variant	rs28627638
Chromosome Location	chr21:17124510-17124511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:17123698..17126562-chr21:17142609..17145221,2	MCF-7	breast:
2	chr21:17104177..17106318-chr21:17123933..17125566,2	K562	blood:
3	chr21:17102350..17105296-chr21:17124464..17127138,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10482874	1.00[EUR][1000 genomes]
rs11911651	1.00[EUR][1000 genomes]
rs1474736	1.00[EUR][1000 genomes]
rs16988288	1.00[EUR][1000 genomes]
rs2225401	1.00[EUR][1000 genomes]
rs2823401	1.00[EUR][1000 genomes]
rs2823409	1.00[EUR][1000 genomes]
rs2823410	1.00[EUR][1000 genomes]
rs2823437	1.00[EUR][1000 genomes]
rs2823439	1.00[EUR][1000 genomes]
rs2823442	1.00[EUR][1000 genomes]
rs2823448	1.00[EUR][1000 genomes]
rs2823450	1.00[EUR][1000 genomes]
rs28372331	1.00[EUR][1000 genomes]
rs28465005	1.00[EUR][1000 genomes]
rs28510398	1.00[EUR][1000 genomes]
rs28542389	1.00[EUR][1000 genomes]
rs28542431	1.00[EUR][1000 genomes]
rs57348380	1.00[EUR][1000 genomes]
rs58963354	1.00[EUR][1000 genomes]
rs61348938	1.00[EUR][1000 genomes]
rs6517555	1.00[EUR][1000 genomes]
rs7281995	1.00[EUR][1000 genomes]
rs7282463	1.00[EUR][1000 genomes]
rs73355441	1.00[EUR][1000 genomes]
rs73360907	1.00[EUR][1000 genomes]
rs73360910	1.00[EUR][1000 genomes]
rs73360912	1.00[EUR][1000 genomes]
rs73360916	1.00[EUR][1000 genomes]
rs7364033	1.00[EUR][1000 genomes]
rs7510266	1.00[EUR][1000 genomes]
rs8126822	1.00[EUR][1000 genomes]
rs8127197	1.00[EUR][1000 genomes]
rs8129950	1.00[EUR][1000 genomes]
rs8130259	1.00[EUR][1000 genomes]
rs8131104	1.00[EUR][1000 genomes]
rs995121	1.00[EUR][1000 genomes]
rs9974439	1.00[EUR][1000 genomes]
rs9974570	1.00[EUR][1000 genomes]
rs9977583	1.00[EUR][1000 genomes]
rs9977671	1.00[EUR][1000 genomes]
rs9978819	1.00[EUR][1000 genomes]
rs9979887	1.00[EUR][1000 genomes]
rs9980143	1.00[EUR][1000 genomes]
rs9981034	1.00[EUR][1000 genomes]
rs9981661	1.00[EUR][1000 genomes]
rs9982635	1.00[EUR][1000 genomes]
rs9983023	1.00[EUR][1000 genomes]
rs9983852	1.00[EUR][1000 genomes]
rs9983961	1.00[EUR][1000 genomes]
rs9984675	1.00[EUR][1000 genomes]
rs9984939	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv275197	chr21:17123855-17130358	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
2	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
3	chr21:17113400-17124800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr21:17114800-17126600	Weak transcription	Aorta	Aorta
5	chr21:17114800-17126600	Weak transcription	NH-A	brain
6	chr21:17115000-17126600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr21:17115200-17130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
9	chr21:17115600-17133400	Weak transcription	Dnd41	blood
10	chr21:17115600-17139400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:17115800-17125600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr21:17116000-17125400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr21:17116200-17124800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:17116200-17139400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:17116400-17125400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:17116600-17124800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr21:17116600-17124800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:17116600-17125400	Weak transcription	Fetal Muscle Leg	muscle
19	chr21:17116600-17125400	Weak transcription	Fetal Stomach	stomach
20	chr21:17116600-17125400	Weak transcription	Right Ventricle	heart
21	chr21:17116600-17125400	Weak transcription	Thymus	Thymus
22	chr21:17116600-17145400	Weak transcription	Esophagus	oesophagus
23	chr21:17116800-17124800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:17117400-17125400	Weak transcription	Placenta	Placenta
25	chr21:17117400-17126400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr21:17119000-17125200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr21:17120800-17124600	Weak transcription	Spleen	Spleen
28	chr21:17121400-17125400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:17121400-17125600	Weak transcription	Fetal Brain Female	brain
30	chr21:17121600-17125200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr21:17121800-17125200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr21:17122000-17125000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr21:17122200-17125200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr21:17122200-17126400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr21:17122200-17126600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr21:17122200-17126600	Weak transcription	Fetal Kidney	kidney
37	chr21:17122200-17127200	Enhancers	Psoas Muscle	Psoas
38	chr21:17122200-17129200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr21:17122400-17124800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr21:17122400-17124800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr21:17122400-17125000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr21:17122400-17125000	Weak transcription	HUVEC	blood vessel
43	chr21:17122400-17125400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr21:17122400-17125400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr21:17122400-17125400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr21:17122400-17126400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr21:17122400-17126600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr21:17122400-17126600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr21:17122400-17126600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr21:17122400-17126600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links