Variant report

Variant	rs4852983
Chromosome Location	chr2:74058894-74058895
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74055980..74060254-chr2:74070607..74073353,3	MCF-7	breast:
2	chr2:74056698..74058945-chr2:74079558..74081408,2	MCF-7	breast:
3	chr2:74058605..74060503-chr2:74157375..74158892,2	K562	blood:
4	chr2:74057033..74061162-chr2:74063972..74066162,5	K562	blood:
5	chr2:74055188..74061210-chr2:74210942..74215230,5	K562	blood:
6	chr2:74058326..74059914-chr2:75062118..75065073,2	K562	blood:
7	chr2:74052797..74060455-chr2:74207744..74214705,21	MCF-7	breast:
8	chr2:74058276..74060848-chr2:74077343..74080264,3	K562	blood:
9	chr2:74055282..74057675-chr2:74058681..74061508,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159399	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1036113	0.93[ASW][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1474335	0.86[CEU][hapmap];0.89[GIH][hapmap]
rs17009428	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs33990056	0.83[EUR][1000 genomes]
rs3738846	0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap]
rs3813229	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813230	0.82[MEX][hapmap]
rs6546875	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6722659	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6726010	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6737597	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs7566009	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7594485	0.93[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][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	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
2	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
3	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4852983	ALMS1	cis	cerebellum	SCAN
rs4852983	ALMS1P	cis	parietal	SCAN
rs4852983	ALMS1P	cis	cerebellum	SCAN
rs4852983	ALMS1	cis	parietal	SCAN
rs4852983	STAMBP	cis	uninvolved skin	skin_eQTL
rs4852983	STAMBP	cis	normal skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74056800-74059000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:74056800-74059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:74056800-74059800	Weak transcription	Aorta	Aorta
4	chr2:74056800-74059800	Weak transcription	Esophagus	oesophagus
5	chr2:74057000-74059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:74057000-74059800	Weak transcription	Gastric	stomach
7	chr2:74057000-74059800	Weak transcription	Ovary	ovary
8	chr2:74057000-74059800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:74057000-74059800	Weak transcription	Thymus	Thymus
10	chr2:74057000-74059800	Weak transcription	Spleen	Spleen
11	chr2:74057000-74060200	Weak transcription	Left Ventricle	heart
12	chr2:74057000-74061800	Weak transcription	Lung	lung
13	chr2:74057000-74063400	Weak transcription	Right Atrium	heart
14	chr2:74057000-74069400	Weak transcription	Colonic Mucosa	Colon
15	chr2:74057000-74076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:74057000-74093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:74057200-74059000	Enhancers	NHDF-Ad	bronchial
18	chr2:74057200-74059400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:74057200-74059400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:74057200-74059400	Weak transcription	Right Ventricle	heart
21	chr2:74057200-74059600	Weak transcription	Fetal Lung	lung
22	chr2:74057200-74061800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:74057200-74062000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:74057400-74059000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:74057400-74059600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:74057400-74059600	Weak transcription	Fetal Brain Male	brain
27	chr2:74057400-74059600	Weak transcription	Fetal Heart	heart
28	chr2:74057400-74059800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:74057400-74059800	Weak transcription	Adipose Nuclei	Adipose
30	chr2:74057400-74060200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:74057400-74063400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:74057600-74059400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:74057600-74059800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:74057600-74071400	Weak transcription	Fetal Kidney	kidney
35	chr2:74057800-74059400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:74057800-74059600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:74057800-74059600	Weak transcription	Brain Germinal Matrix	brain
38	chr2:74057800-74061000	Genic enhancers	Dnd41	blood
39	chr2:74057800-74063600	Weak transcription	Fetal Brain Female	brain
40	chr2:74058000-74059000	Genic enhancers	Brain Substantia Nigra	brain
41	chr2:74058000-74059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:74058000-74059600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:74058000-74059800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:74058000-74060000	Strong transcription	Fetal Thymus	thymus
45	chr2:74058000-74061200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:74058000-74062200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:74058000-74062400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr2:74058000-74062400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:74058000-74064200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:74058000-74064200	Strong transcription	Fetal Intestine Large	intestine

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