Variant report

Variant	rs56246741
Chromosome Location	chr3:67572346-67572347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67571229..67573856-chr3:67577738..67580232,2	K562	blood:

Variant related genes	Relation type
ENSG00000172340	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11919650	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11919747	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11923127	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11927204	0.91[EUR][1000 genomes]
rs12488930	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12489287	0.87[EUR][1000 genomes]
rs12495506	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12636825	0.88[EUR][1000 genomes]
rs17046528	0.95[EUR][1000 genomes]
rs17046546	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17046548	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4371532	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856869	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856870	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4856872	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4856873	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4856874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4856875	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5028414	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56020437	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56361934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58093651	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61386974	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6548615	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6768958	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6784255	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72923195	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72924913	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7623441	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
2	chr3:67521600-67580400	Weak transcription	Stomach Mucosa	stomach
3	chr3:67526800-67583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:67531400-67576200	Weak transcription	HMEC	breast
5	chr3:67533200-67577000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:67533400-67577600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:67534400-67576400	Weak transcription	Aorta	Aorta
8	chr3:67535000-67578800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:67537400-67579600	Weak transcription	Small Intestine	intestine
10	chr3:67541400-67582000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:67544200-67580200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:67544800-67577600	Weak transcription	Thymus	Thymus
13	chr3:67553800-67579600	Weak transcription	Hela-S3	cervix
14	chr3:67554600-67577800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:67555800-67579600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:67557400-67583200	Weak transcription	K562	blood
17	chr3:67558400-67580200	Weak transcription	Fetal Thymus	thymus
18	chr3:67559600-67577600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:67560200-67581800	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:67560400-67577600	Weak transcription	Right Ventricle	heart
21	chr3:67560600-67576800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:67560600-67580200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:67560600-67586200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
25	chr3:67561800-67579400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:67563800-67580800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:67564600-67579800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:67564800-67580400	Weak transcription	Brain Anterior Caudate	brain
29	chr3:67565000-67580200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:67565200-67577600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:67565400-67577400	Weak transcription	A549	lung
32	chr3:67565600-67576200	Weak transcription	Osteobl	bone
33	chr3:67565600-67577000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:67565600-67577400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:67565600-67579800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:67565600-67595800	Weak transcription	Fetal Kidney	kidney
37	chr3:67566600-67581000	Weak transcription	Gastric	stomach
38	chr3:67566800-67580200	Weak transcription	HUVEC	blood vessel
39	chr3:67566800-67581800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:67566800-67582000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:67567000-67581200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:67567000-67581800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:67567200-67579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:67567200-67581400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:67567400-67576800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:67567400-67577600	Weak transcription	Fetal Stomach	stomach
47	chr3:67567400-67577600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:67567400-67577800	Weak transcription	Pancreas	Pancrea
49	chr3:67567600-67576200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:67568000-67576200	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links