Variant report

Variant	rs17241402
Chromosome Location	chr21:17114034-17114035
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	chr21:17101726..17104048-chr21:17113202..17115443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11909953	0.84[CHB][hapmap]
rs13347185	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17307156	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986788	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2823464	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2823467	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823473	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823477	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823479	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823480	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823487	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2823488	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28484960	0.81[ASN][1000 genomes]
rs28553297	0.81[ASN][1000 genomes]
rs28730511	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55804442	0.93[ASN][1000 genomes]
rs58134477	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58683309	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60174740	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6517612	0.92[CHB][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7277813	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8128335	1.00[CEU][hapmap]
rs8130607	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8132755	0.81[ASN][1000 genomes]
rs926612	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9305754	0.84[CHB][hapmap]
rs9680115	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977019	0.84[CHB][hapmap]

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	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17103200-17114400	Weak transcription	Spleen	Spleen
2	chr21:17103400-17114400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:17103800-17114400	Weak transcription	Lung	lung
4	chr21:17103800-17115000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:17104000-17114600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:17104000-17114600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr21:17104200-17133400	Weak transcription	Colonic Mucosa	Colon
8	chr21:17104600-17114600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr21:17104600-17123400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr21:17104800-17115000	Weak transcription	Fetal Muscle Leg	muscle
11	chr21:17105400-17114400	Weak transcription	Brain Germinal Matrix	brain
12	chr21:17105400-17114800	Weak transcription	Fetal Stomach	stomach
13	chr21:17105400-17115000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr21:17105400-17115200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr21:17105400-17119400	Weak transcription	Brain Angular Gyrus	brain
16	chr21:17105400-17125200	Weak transcription	Brain Substantia Nigra	brain
17	chr21:17105800-17114600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr21:17106000-17114400	Weak transcription	Gastric	stomach
19	chr21:17106000-17114600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr21:17106200-17114800	Weak transcription	Fetal Thymus	thymus
21	chr21:17106400-17114800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr21:17106400-17115200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr21:17106600-17114800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr21:17106600-17116600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr21:17106800-17115200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr21:17108000-17114800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:17108200-17114800	Weak transcription	Fetal Intestine Small	intestine
28	chr21:17108600-17114400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr21:17108600-17115000	Weak transcription	Placenta	Placenta
30	chr21:17108600-17115000	Weak transcription	Thymus	Thymus
31	chr21:17108800-17114400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr21:17108800-17114800	Weak transcription	Dnd41	blood
33	chr21:17108800-17115200	Enhancers	HUVEC	blood vessel
34	chr21:17109400-17121000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr21:17110000-17115000	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr21:17111400-17115000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr21:17111600-17117800	Enhancers	K562	blood
38	chr21:17111800-17115200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr21:17111800-17115200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr21:17112000-17114200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr21:17112000-17114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr21:17112000-17114400	Weak transcription	Pancreas	Pancrea
43	chr21:17112000-17114400	Weak transcription	Right Atrium	heart
44	chr21:17112000-17114600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr21:17112000-17114600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr21:17112000-17114600	Weak transcription	Esophagus	oesophagus
47	chr21:17112000-17114600	Weak transcription	Left Ventricle	heart
48	chr21:17112000-17114800	Weak transcription	Fetal Intestine Large	intestine
49	chr21:17112000-17115400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr21:17112200-17114400	Enhancers	Pancreatic Islets	Pancreatic Islet

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