Variant report

Variant	rs2567600
Chromosome Location	chr2:73981598-73981599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr2:73981467-73981767	K562	blood:	n/a	n/a
2	USF1	chr2:73981542-73981722	GM12878	blood:	n/a	chr2:73981640-73981651
3	JUND	chr2:73981545-73981765	HepG2	liver:	n/a	n/a
4	JUND	chr2:73981487-73981768	K562	blood:	n/a	n/a
5	USF1	chr2:73981406-73981848	A549	lung:	n/a	chr2:73981640-73981651
6	USF1	chr2:73981441-73981751	K562	blood:	n/a	chr2:73981640-73981651
7	POLR2A	chr2:73981526-73981721	GM12878	blood:	n/a	n/a
8	USF1	chr2:73981535-73981755	HepG2	liver:	n/a	chr2:73981640-73981651
9	FOSL2	chr2:73981512-73981852	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:73981515-73982049	GM12878	blood:	n/a	n/a
11	USF1	chr2:73981535-73981735	HepG2	liver:	n/a	chr2:73981640-73981651
12	POLR2A	chr2:73981398-73981676	K562	blood:	n/a	n/a
13	USF1	chr2:73981448-73981887	K562	blood:	n/a	chr2:73981640-73981651

No.	Distal block	Cell Line	Cell type
1	chr2:73963336..73965581-chr2:73980235..73982891,2	K562	blood:
2	chr2:73981031..73983737-chr2:73985757..73987804,3	K562	blood:
3	chr2:73979494..73982324-chr2:74005407..74007165,2	K562	blood:
4	chr2:73980953..73983129-chr2:73987298..73988950,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf78-3	chr2:73981095-73981974	NONHSAT071632

Variant related genes	Relation type
ENSG00000273245	TF binding region
ENSG00000144048	Chromatin interaction
ENSG00000144034	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2567598	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2567601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2567602	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2567603	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
5	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv998315	chr2:73919185-74003998	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2567600	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2567600	ALMS1P	cis	Nerve Tibial	GTEx
rs2567600	ALMS1P	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73964600-74005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:73965000-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:73965400-73982200	Weak transcription	Hela-S3	cervix
4	chr2:73965400-73985600	Weak transcription	Fetal Heart	heart
5	chr2:73965400-73986200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:73965400-73986600	Weak transcription	Psoas Muscle	Psoas
7	chr2:73966200-73992000	Weak transcription	Stomach Mucosa	stomach
8	chr2:73969400-73983400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:73969400-73987200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:73969600-73986000	Weak transcription	Right Ventricle	heart
11	chr2:73969800-73982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:73969800-73982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:73971400-74002200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:73971600-73987000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:73972000-73992200	Weak transcription	Fetal Kidney	kidney
16	chr2:73973400-73982200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:73973400-73987400	Weak transcription	Colonic Mucosa	Colon
18	chr2:73973800-73982200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:73974000-73983400	Weak transcription	Pancreas	Pancrea
20	chr2:73974000-73984800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:73974000-73984800	Weak transcription	Esophagus	oesophagus
22	chr2:73974000-73986000	Weak transcription	Small Intestine	intestine
23	chr2:73974000-73989000	Weak transcription	Fetal Brain Male	brain
24	chr2:73974200-73982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:73974200-73984600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:73974200-73986800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:73974400-73982200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:73974400-73987000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:73974600-73985800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:73975400-73981800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:73976400-73986200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:73976600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:73977000-73984000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:73977200-73995000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:73977400-73985600	Strong transcription	Adipose Nuclei	Adipose
36	chr2:73977400-73986000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:73977400-73986400	Strong transcription	Fetal Muscle Leg	muscle
38	chr2:73977400-73993000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:73977400-74001400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:73977400-74004800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:73977600-74004800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:73977800-74004000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:73978000-74004200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:73978200-73982200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:73978200-73983400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:73978200-73998400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:73978400-73984600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:73978600-73983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:73978800-73995200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:73979200-73983400	Weak transcription	Gastric	stomach

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