Variant report

Variant	rs7551698
Chromosome Location	chr1:45504720-45504721
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45503364..45509535-chr1:45510898..45517046,6	K562	blood:
2	chr1:45185795..45187646-chr1:45502768..45506079,3	K562	blood:
3	chr1:45500321..45502356-chr1:45502649..45504845,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10736425	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10890319	0.95[AFR][1000 genomes]
rs11211067	0.81[YRI][hapmap]
rs11211072	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047556	0.95[AFR][1000 genomes]
rs12094272	0.93[AFR][1000 genomes]
rs2298006	0.89[AFR][1000 genomes]
rs264011	0.85[YRI][hapmap]
rs264014	0.82[YRI][hapmap]
rs6666806	0.89[YRI][hapmap]
rs6671633	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs7537361	0.95[AFR][1000 genomes]
rs7543818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7551698	ZSWIM5	cis	brain	BrainEAC
rs7551698	ZSWIM5	cis	cerebellar cortex	BrainEAC
rs7551698	ZSWIM5	cis	occipital cortex	BrainEAC
rs7551698	ZSWIM5	cis	frontal cortex	BrainEAC
rs7551698	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs7551698	ZSWIM5	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45480800-45510400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:45481200-45510200	Weak transcription	Lung	lung
3	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
5	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
7	chr1:45492000-45507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:45495000-45506800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:45497400-45525400	Weak transcription	Gastric	stomach
10	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
11	chr1:45498200-45506800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:45500000-45504800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:45500400-45505200	Weak transcription	Right Ventricle	heart
15	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
17	chr1:45501600-45504800	Enhancers	Fetal Intestine Large	intestine
18	chr1:45501800-45505800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:45501800-45508000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:45501800-45516200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
23	chr1:45502000-45507600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:45502000-45507600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:45502000-45508000	Weak transcription	Brain Angular Gyrus	brain
26	chr1:45502000-45508000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:45502000-45508000	Weak transcription	Fetal Brain Female	brain
28	chr1:45502000-45508200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:45502000-45508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:45502000-45510600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:45502000-45512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:45502400-45505200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:45502400-45507800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
36	chr1:45503400-45508200	Weak transcription	Brain Anterior Caudate	brain
37	chr1:45503600-45505200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:45503800-45504800	Strong transcription	Ovary	ovary
39	chr1:45504000-45505200	Genic enhancers	HepG2	liver
40	chr1:45504000-45509800	Strong transcription	Brain Germinal Matrix	brain
41	chr1:45504000-45510400	Weak transcription	Hela-S3	cervix
42	chr1:45504200-45505000	Strong transcription	Fetal Stomach	stomach
43	chr1:45504200-45505800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
45	chr1:45504400-45505000	Flanking Active TSS	K562	blood
46	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:45504600-45504800	Enhancers	Colonic Mucosa	Colon
48	chr1:45504600-45505200	Strong transcription	Fetal Intestine Small	intestine
49	chr1:45504600-45508400	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links