Variant report

Variant	rs17004508
Chromosome Location	chr21:45213385-45213386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:45212818-45213937	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr21:45213182-45214037	K562	blood:	n/a	n/a
3	HEY1	chr21:45213029-45213646	K562	blood:	n/a	chr21:45213313-45213328
4	POLR2A	chr21:45213005-45215207	K562	blood:	n/a	n/a
5	POLR2A	chr21:45213291-45215222	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45213183..45215039-chr21:45229928..45232501,2	MCF-7	breast:
2	chr21:45208995..45211029-chr21:45212842..45214675,3	MCF-7	breast:
3	chr21:45210899..45216228-chr21:45227595..45230862,5	MCF-7	breast:
4	chr21:45188590..45190206-chr21:45212982..45214484,2	MCF-7	breast:

Variant related genes	Relation type
RRP1	TF binding region
ENSG00000160214	Chromatin interaction
ENSG00000215458	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2838392	0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28581805	1.00[ASN][1000 genomes]
rs58194014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58549917	1.00[ASN][1000 genomes]
rs743467	1.00[ASN][1000 genomes]
rs8128568	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv913879	chr21:45145286-45237039	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
11	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv913885	chr21:45206355-45249474	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv587718	chr21:45210932-45252838	Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1065007	chr21:45212880-45257959	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv544470	chr21:45212880-45257959	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45210400-45216600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:45210400-45221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:45210800-45213600	Genic enhancers	Brain Germinal Matrix	brain
4	chr21:45210800-45214000	Weak transcription	Psoas Muscle	Psoas
5	chr21:45210800-45216200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr21:45211000-45214200	Strong transcription	NH-A	brain
7	chr21:45211000-45215400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:45211000-45215400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:45211000-45215400	Strong transcription	NHLF	lung
10	chr21:45211000-45215600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr21:45211000-45217600	Strong transcription	NHDF-Ad	bronchial
12	chr21:45211000-45219200	Weak transcription	Fetal Heart	heart
13	chr21:45211000-45223200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr21:45211000-45224200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:45211000-45224200	Strong transcription	Osteobl	bone
16	chr21:45211000-45224800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr21:45211000-45224800	Strong transcription	Brain Hippocampus Middle	brain
18	chr21:45211000-45224800	Strong transcription	Placenta	Placenta
19	chr21:45211000-45226200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr21:45211000-45226200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr21:45211000-45226600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr21:45211000-45226600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr21:45211000-45229200	Strong transcription	Fetal Intestine Small	intestine
24	chr21:45211000-45230400	Weak transcription	Stomach Mucosa	stomach
25	chr21:45211000-45257200	Weak transcription	Right Atrium	heart
26	chr21:45211200-45213400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr21:45211200-45214000	Strong transcription	Fetal Lung	lung
28	chr21:45211200-45214400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr21:45211200-45221800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr21:45211200-45223400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr21:45211200-45224000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr21:45211200-45224400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr21:45211200-45224400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr21:45211200-45224400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr21:45211200-45224600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr21:45211200-45224600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr21:45211200-45224800	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr21:45211200-45224800	Strong transcription	Ovary	ovary
39	chr21:45211200-45225000	Strong transcription	Right Ventricle	heart
40	chr21:45211200-45225200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr21:45211200-45226200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr21:45211200-45226400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr21:45211200-45226800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr21:45211200-45226800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:45211200-45226800	Strong transcription	Esophagus	oesophagus
46	chr21:45211200-45227000	Strong transcription	Primary T cells from cord blood	blood
47	chr21:45211200-45227200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:45211200-45227200	Strong transcription	NHEK	skin
49	chr21:45211200-45229400	Strong transcription	Fetal Stomach	stomach
50	chr21:45211200-45230600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links