Variant report

Variant	rs2229465
Chromosome Location	chr1:209799205-209799206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr1:209799171-209799261	Hela-S3	cervix:	n/a	n/a
2	JUND	chr1:209798289-209799266	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:209798261-209801629	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:209799191-209799241	NHBE	bronchial:	n/a
2	chr1:209799191-209799241	T-47D	breast:	n/a
3	chr1:209799191-209799241	Jurkat	blood:	n/a
4	chr1:209799191-209799241	RPTEC	kidney:	n/a
5	chr1:209799191-209799241	SKMC	muscle:	n/a
6	chr1:209799191-209799241	GM12878	blood:	n/a
7	chr1:209799191-209799241	PrEC	prostate:	n/a
8	chr1:209799191-209799241	AG10803	skin:	n/a
9	chr1:209799191-209799241	HRE	kidney:	n/a
10	chr1:209799191-209799241	AG09309	skin:	n/a
11	chr1:209799191-209799241	NB4	blood:	n/a
12	chr1:209799191-209799241	Hepatocyte	liver:	n/a
13	chr1:209799191-209799241	ECC-1	luminal epithelium:	n/a
14	chr1:209799191-209799241	SK-N-SH_RA	brain:	n/a
15	chr1:209799191-209799241	AoSMC	blood vessel:	n/a
16	chr1:209799191-209799241	HEK293	kidney:	embryo
17	chr1:209799191-209799241	IMR90	lung:	fetal
18	chr1:209799191-209799241	ProgFib	skin:	n/a
19	chr1:209799191-209799241	GM19239	blood:	n/a
20	chr1:209799191-209799241	HL-60	blood:	n/a
21	chr1:209799191-209799241	Hela-S3	cervix:	n/a
22	chr1:209799191-209799241	BJ	skin:	n/a
23	chr1:209799191-209799241	CMK	blood:	n/a
24	chr1:209799191-209799241	NH-A	brain:	n/a
25	chr1:209799191-209799241	HMEC	breast:	n/a
26	chr1:209799191-209799241	H1-hESC	embryonic stem cell:	embryo
27	chr1:209799191-209799241	HAEpiC	amniotic membrane:	n/a
28	chr1:209799191-209799241	HCPEpiC	choroid plexus:	n/a
29	chr1:209799191-209799241	AG09319	gingival:	n/a
30	chr1:209799191-209799241	MCF-7	breast:	n/a
31	chr1:209799191-209799241	HIPEpiC	eye:	n/a
32	chr1:209799191-209799241	HRPEpiC	eye:	n/a
33	chr1:209799191-209799241	SAEC	small airway:	n/a
34	chr1:209799191-209799241	HUVEC	blood vessel:	n/a
35	chr1:209799191-209799241	HCM	heart:	n/a
36	chr1:209799191-209799241	GM12891	blood:	n/a
37	chr1:209799191-209799241	MCF10A-Er-Src	breast:	n/a
38	chr1:209799191-209799241	A549	lung:	n/a
39	chr1:209799191-209799241	HNPCEpiC	eye:	n/a
40	chr1:209799191-209799241	ovcar-3	ovarian:	n/a
41	chr1:209799191-209799241	PFSK-1	brain:	n/a
42	chr1:209799191-209799241	HRCEpiC	kidney:	n/a
43	chr1:209799191-209799241	GM12892	blood:	n/a
44	chr1:209799191-209799241	LNCaP	prostate:	n/a
45	chr1:209799191-209799241	NT2-D1	testis:	n/a
46	chr1:209799191-209799241	U87	brain:	n/a
47	chr1:209799191-209799241	BE2_C	brain:	n/a
48	chr1:209799191-209799241	HPAEpiC	pulmonary alveolar:	n/a
49	chr1:209799191-209799241	HCF	heart:	n/a
50	chr1:209799191-209799241	HCT-116	colon:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209788000..209789545-chr1:209798332..209800305,2	K562	blood:
2	chr1:209793195..209794900-chr1:209798885..209800894,2	K562	blood:

No data

Variant related genes	Relation type
MIR4260	TF binding region
MIR4260	CpG island

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489340	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12073223	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12090288	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12403733	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12410975	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs17014889	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17014906	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17014942	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17014955	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17015006	0.82[MEX][hapmap]
rs2072937	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2072939	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2072942	0.87[AMR][1000 genomes]
rs2076219	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2076222	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2076232	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2076347	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2076348	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2076349	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs2076352	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2229466	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2235542	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes]
rs2236889	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2236890	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2282734	0.87[AMR][1000 genomes]
rs2282736	0.87[AMR][1000 genomes]
rs2282737	0.87[AMR][1000 genomes]
rs58679997	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59815577	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60927005	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs714971	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209786800-209800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:209787200-209808400	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr1:209787400-209816200	Strong transcription	NHEK	skin
4	chr1:209789000-209802800	Strong transcription	Hela-S3	cervix
5	chr1:209791800-209801400	Enhancers	Fetal Muscle Leg	muscle
6	chr1:209792400-209806400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:209793000-209801600	Enhancers	Ovary	ovary
8	chr1:209793600-209801600	Enhancers	Spleen	Spleen
9	chr1:209793800-209800000	Weak transcription	Lung	lung
10	chr1:209794200-209799600	Weak transcription	Stomach Mucosa	stomach
11	chr1:209794800-209803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:209795200-209799600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:209795200-209804400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:209795400-209799600	Weak transcription	Liver	Liver
15	chr1:209795600-209800800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:209796000-209800800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:209796000-209801000	Weak transcription	Pancreas	Pancrea
18	chr1:209796200-209799400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:209796200-209800800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:209796400-209799400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:209796400-209800200	Strong transcription	Colonic Mucosa	Colon
22	chr1:209796400-209800800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:209796400-209801000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:209797000-209801400	Enhancers	Fetal Heart	heart
25	chr1:209797000-209801600	Enhancers	Right Ventricle	heart
26	chr1:209797200-209800000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:209797800-209801600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr1:209797800-209803200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:209798000-209801400	Enhancers	HSMMtube	muscle
30	chr1:209798000-209805200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:209798200-209800800	Strong transcription	Fetal Stomach	stomach
32	chr1:209798200-209801600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:209798400-209799400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:209798400-209800000	Genic enhancers	Fetal Intestine Large	intestine
35	chr1:209798400-209800400	Enhancers	Adipose Nuclei	Adipose
36	chr1:209798400-209801400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:209798400-209801600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:209798400-209801600	Enhancers	Left Ventricle	heart
39	chr1:209798600-209799400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:209798600-209799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:209798600-209799800	Genic enhancers	Fetal Intestine Small	intestine
42	chr1:209798600-209801600	Enhancers	Stomach Smooth Muscle	stomach
43	chr1:209798800-209799400	Flanking Active TSS	HSMM	muscle
44	chr1:209798800-209801200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:209798800-209801200	Enhancers	Fetal Brain Female	brain
46	chr1:209798800-209801600	Enhancers	Brain Cingulate Gyrus	brain
47	chr1:209798800-209801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:209798800-209801600	Strong transcription	Gastric	stomach
49	chr1:209799000-209799600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:209799000-209800200	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links