Variant report

Variant	rs56220401
Chromosome Location	chr2:153437901-153437902
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153437360..153438992-chr2:153441659..153443672,2	MCF-7	breast:
2	chr2:153431363..153434318-chr2:153436481..153440010,3	K562	blood:
3	chr2:153431392..153434318-chr2:153435903..153437981,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10497107	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497108	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497111	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892222	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1370500	0.88[EUR][1000 genomes]
rs1370501	0.85[EUR][1000 genomes]
rs16823807	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823809	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16823813	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16831392	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831399	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831410	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811572	1.00[ASN][1000 genomes]
rs57173254	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58383962	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59103281	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61698095	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573833	1.00[ASN][1000 genomes]
rs7599894	0.98[EUR][1000 genomes]
rs7600114	0.98[EUR][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	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153400000-153438000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:153400000-153468200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:153400600-153442000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:153403200-153448000	Weak transcription	Lung	lung
5	chr2:153404200-153442400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:153405200-153441800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:153415000-153438200	Weak transcription	Fetal Lung	lung
8	chr2:153416400-153438000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:153416400-153454200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:153416400-153465200	Weak transcription	Left Ventricle	heart
11	chr2:153417800-153442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:153418800-153444600	Weak transcription	Fetal Brain Male	brain
13	chr2:153419600-153438000	Weak transcription	Fetal Intestine Large	intestine
14	chr2:153420400-153443400	Weak transcription	Fetal Intestine Small	intestine
15	chr2:153423800-153471200	Weak transcription	Fetal Kidney	kidney
16	chr2:153425200-153438000	Weak transcription	Fetal Brain Female	brain
17	chr2:153425600-153438200	Enhancers	Brain Hippocampus Middle	brain
18	chr2:153428000-153438000	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:153428000-153442000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:153428000-153468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:153428200-153440000	Weak transcription	Fetal Heart	heart
22	chr2:153428200-153456000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:153429200-153456200	Weak transcription	Spleen	Spleen
24	chr2:153429600-153442200	Strong transcription	HepG2	liver
25	chr2:153429800-153439600	Weak transcription	A549	lung
26	chr2:153430000-153440200	Weak transcription	NH-A	brain
27	chr2:153430000-153449400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:153430200-153438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:153430200-153440800	Weak transcription	NHLF	lung
30	chr2:153430400-153441200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:153431400-153438000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:153433400-153438600	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:153433600-153438000	Weak transcription	NHEK	skin
34	chr2:153434000-153438000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:153434200-153438000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:153434200-153438000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:153434200-153442600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:153434200-153473600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:153434400-153439600	Weak transcription	Aorta	Aorta
40	chr2:153434400-153440000	Weak transcription	Psoas Muscle	Psoas
41	chr2:153434400-153442000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:153434400-153454400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:153434600-153438000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:153434600-153442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:153434600-153442400	Weak transcription	Small Intestine	intestine
46	chr2:153434800-153441400	Weak transcription	Ovary	ovary
47	chr2:153435200-153441600	Enhancers	Brain Substantia Nigra	brain
48	chr2:153435400-153473200	Weak transcription	Right Ventricle	heart
49	chr2:153435600-153455200	Weak transcription	Hela-S3	cervix
50	chr2:153436400-153438200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links