Variant report

Variant	rs330550
Chromosome Location	chr13:111268633-111268634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49412567..49413110-chr13:111268213..111268896,2	Hela-S3	cervix:
2	chr13:111158551..111160525-chr13:111267801..111269585,2	MCF-7	breast:
3	chr13:111266678..111269187-chr13:111295319..111298212,3	MCF-7	breast:
4	chr13:111266655..111268705-chr13:111294879..111298471,3	K562	blood:
5	chr13:111266587..111269692-chr13:111357018..111359356,4	K562	blood:
6	chr13:111265515..111270086-chr13:111364987..111368051,5	MCF-7	breast:
7	chr13:111268021..111270238-chr13:111291368..111294151,2	MCF-7	breast:
8	chr13:111268194..111268777-chr6:12010640..12011635,2	Hela-S3	cervix:
9	chr13:111268040..111269954-chr13:111270156..111273298,3	K562	blood:
10	chr13:111266965..111271727-chr13:111364973..111369025,9	MCF-7	breast:
11	chr13:111266746..111269387-chr13:111357064..111359748,3	MCF-7	breast:
12	chr13:111267596..111269197-chr13:111364131..111366094,2	K562	blood:
13	chr13:111267467..111269967-chr13:111564590..111568374,3	MCF-7	breast:
14	chr13:111266944..111268705-chr13:111296076..111298471,2	K562	blood:
15	chr13:111265756..111270693-chr13:111363417..111370660,10	K562	blood:
16	chr13:111267851..111270253-chr13:111566067..111568371,3	K562	blood:
17	chr13:111266737..111268751-chr13:111366724..111368921,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134871	Chromatin interaction
ENSG00000088448	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000255831	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2765346	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766501	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2986321	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330554	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs330556	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330558	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330563	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs330564	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs330566	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs381033	0.82[EUR][1000 genomes]
rs392660	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs403908	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs424649	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs441805	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61970485	0.95[EUR][1000 genomes]
rs7394	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7998306	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1038089	chr13:111229517-111274823	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
14	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
15	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
18	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription 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	240 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs330550	CARS2	cis	lymphoblastoid	seeQTL
rs330550	AL139385.1	cis	Muscle Skeletal	GTEx
rs330550	CARKD	cis	Muscle Skeletal	GTEx
rs330550	CARKD	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111267000-111269000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr13:111267200-111268800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr13:111267200-111268800	Active TSS	Brain Anterior Caudate	brain
4	chr13:111267200-111268800	Active TSS	HSMMtube	muscle
5	chr13:111267200-111268800	Active TSS	NHLF	lung
6	chr13:111267200-111269000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:111267200-111269000	Active TSS	Rectal Smooth Muscle	rectum
8	chr13:111267200-111269400	Active TSS	A549	lung
9	chr13:111267200-111270000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:111267400-111268800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr13:111267400-111268800	Active TSS	Primary T cells from cord blood	blood
12	chr13:111267400-111268800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:111267400-111268800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
14	chr13:111267400-111268800	Active TSS	Fetal Brain Female	brain
15	chr13:111267400-111268800	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr13:111267400-111269000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr13:111267400-111269000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr13:111267400-111269000	Active TSS	Brain Angular Gyrus	brain
19	chr13:111267400-111269000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr13:111267400-111269200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr13:111267400-111269200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr13:111267400-111269200	Active TSS	Left Ventricle	heart
23	chr13:111267400-111269200	Active TSS	Right Ventricle	heart
24	chr13:111267400-111269800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr13:111267600-111268800	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr13:111267600-111268800	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr13:111267600-111268800	Active TSS	Colon Smooth Muscle	Colon
28	chr13:111267600-111268800	Active TSS	Fetal Intestine Large	intestine
29	chr13:111267600-111268800	Active TSS	Hela-S3	cervix
30	chr13:111267600-111269000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr13:111267600-111269000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:111267600-111269000	Active TSS	Liver	Liver
33	chr13:111267600-111269200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr13:111267600-111269200	Active TSS	Psoas Muscle	Psoas
35	chr13:111267600-111269400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr13:111267600-111269400	Active TSS	Esophagus	oesophagus
37	chr13:111267600-111269400	Active TSS	Right Atrium	heart
38	chr13:111267800-111268800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr13:111267800-111268800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:111267800-111268800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:111267800-111268800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:111267800-111268800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:111267800-111268800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:111267800-111268800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr13:111267800-111268800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr13:111267800-111268800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:111267800-111268800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:111267800-111268800	Active TSS	Brain Substantia Nigra	brain
49	chr13:111267800-111268800	Weak transcription	Fetal Heart	heart
50	chr13:111267800-111268800	Active TSS	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links