Variant report

Variant	rs2249666
Chromosome Location	chr21:40719241-40719242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr21:40716967-40721099	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr21:40716164-40723345	K562	blood:	n/a	n/a
3	TBL1XR1	chr21:40718919-40720642	K562	blood:	n/a	n/a
4	IRF1	chr21:40718316-40720432	K562	blood:	n/a	n/a
5	IRF1	chr21:40718834-40720511	K562	blood:	n/a	n/a
6	EP300	chr21:40719066-40719265	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24607940..24610732-chr21:40718347..40720759,2	MCF-7	breast:
2	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
3	chr21:40718950..40720909-chr8:144820152..144822605,2	MCF-7	breast:
4	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
5	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
6	chr21:40635414..40638745-chr21:40717382..40720310,3	K562	blood:
7	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
8	chr21:40650313..40652723-chr21:40719146..40721312,2	MCF-7	breast:
9	chr21:40555099..40556872-chr21:40718336..40720047,2	MCF-7	breast:
10	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
11	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
12	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
13	chr21:40719170..40722188-chr21:40780437..40783108,3	MCF-7	breast:
14	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238556	TF binding region
HMGN1	TF binding region
ENSG00000238141	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000259321	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2735307	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735308	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2776306	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2776311	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2776312	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854727	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2989329	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3167757	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs741795	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128901	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8128919	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8132993	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs914156	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9980890	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249666	HMGN1	cis	multi-tissue	Pritchard
rs2249666	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
4	chr21:40715800-40719400	Weak transcription	Ovary	ovary
5	chr21:40715800-40719600	Weak transcription	Esophagus	oesophagus
6	chr21:40716000-40719400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr21:40716000-40719400	Weak transcription	Brain Anterior Caudate	brain
8	chr21:40716000-40719600	Weak transcription	Aorta	Aorta
9	chr21:40716000-40719600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr21:40716000-40719600	Weak transcription	Colonic Mucosa	Colon
11	chr21:40716000-40719600	Weak transcription	Gastric	stomach
12	chr21:40716000-40719600	Weak transcription	Lung	lung
13	chr21:40716000-40719600	Weak transcription	Psoas Muscle	Psoas
14	chr21:40716000-40719600	Weak transcription	Small Intestine	intestine
15	chr21:40716200-40720000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:40716400-40719400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40716400-40720000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr21:40716600-40719600	Weak transcription	Brain Substantia Nigra	brain
19	chr21:40716800-40719800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:40717000-40719400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr21:40717000-40720400	Transcr. at gene 5' and 3'	Dnd41	blood
22	chr21:40717200-40719600	Weak transcription	Left Ventricle	heart
23	chr21:40717200-40719600	Transcr. at gene 5' and 3'	NH-A	brain
24	chr21:40717200-40719800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
25	chr21:40717200-40720000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
26	chr21:40717200-40720200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
27	chr21:40717400-40719400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr21:40717400-40719400	Enhancers	Colon Smooth Muscle	Colon
29	chr21:40717400-40719400	Enhancers	Fetal Brain Male	brain
30	chr21:40717400-40719600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr21:40717400-40719800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
32	chr21:40717400-40720200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr21:40717400-40720400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
34	chr21:40717600-40719600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr21:40717600-40720200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr21:40717600-40720400	Transcr. at gene 5' and 3'	A549	lung
37	chr21:40717600-40720400	Transcr. at gene 5' and 3'	K562	blood
38	chr21:40717800-40719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr21:40717800-40719400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr21:40717800-40719400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr21:40717800-40719400	Weak transcription	Right Ventricle	heart
42	chr21:40717800-40720200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr21:40718000-40719400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr21:40718000-40719400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr21:40718000-40719600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
46	chr21:40718000-40721400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:40718200-40719400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr21:40718200-40719600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr21:40718200-40719600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr21:40718200-40719800	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links