Variant report

Variant	rs4793741
Chromosome Location	chr17:46062560-46062561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46053682..46056585-chr17:46059998..46062709,2	K562	blood:
2	chr17:46059948..46063060-chr17:46063175..46066138,4	MCF-7	breast:
3	chr17:46058631..46063478-chr17:46064617..46070061,8	K562	blood:
4	chr17:46046877..46049388-chr17:46060915..46063110,2	K562	blood:
5	chr17:46062331..46065308-chr17:46079122..46082112,2	K562	blood:
6	chr17:46062331..46065040-chr17:46080612..46082593,2	K562	blood:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17617010	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794318	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4794333	0.91[ASN][1000 genomes]
rs73323378	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082043	0.88[ASN][1000 genomes]
rs886444	0.91[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4793741	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs4793741	SCRN2	cis	Esophagus Mucosa	GTEx
rs4793741	SCRN2	cis	Esophagus Muscularis	GTEx
rs4793741	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
2	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
5	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr17:46050800-46062600	Strong transcription	Fetal Intestine Small	intestine
7	chr17:46050800-46062800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:46050800-46063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr17:46050800-46063000	Strong transcription	Fetal Muscle Leg	muscle
10	chr17:46051000-46063000	Strong transcription	Primary T cells from cord blood	blood
11	chr17:46051000-46063000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:46054200-46063000	Strong transcription	Thymus	Thymus
13	chr17:46056200-46064000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:46056400-46063200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:46057000-46064000	Weak transcription	Fetal Brain Male	brain
16	chr17:46058200-46064400	Weak transcription	Fetal Kidney	kidney
17	chr17:46059000-46064600	Weak transcription	NHDF-Ad	bronchial
18	chr17:46059400-46064000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:46059400-46064600	Weak transcription	HUVEC	blood vessel
20	chr17:46059400-46064800	Weak transcription	Colon Smooth Muscle	Colon
21	chr17:46059600-46064600	Weak transcription	Psoas Muscle	Psoas
22	chr17:46059800-46062600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr17:46059800-46062800	Strong transcription	Fetal Thymus	thymus
24	chr17:46060400-46063600	Weak transcription	Colonic Mucosa	Colon
25	chr17:46060400-46064600	Weak transcription	Fetal Lung	lung
26	chr17:46060400-46065200	Weak transcription	Osteobl	bone
27	chr17:46060600-46063400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:46060600-46063600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:46060600-46063800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:46060600-46064000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr17:46060600-46064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:46060800-46063000	Weak transcription	Ovary	ovary
33	chr17:46060800-46064800	Weak transcription	Lung	lung
34	chr17:46060800-46064800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:46061000-46062800	Strong transcription	Spleen	Spleen
36	chr17:46061000-46062800	Weak transcription	A549	lung
37	chr17:46061000-46063800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr17:46061000-46064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:46061000-46064400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:46061000-46064400	Weak transcription	Stomach Mucosa	stomach
41	chr17:46061000-46064600	Weak transcription	Esophagus	oesophagus
42	chr17:46061000-46064800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr17:46061000-46064800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr17:46061000-46065200	Weak transcription	Brain Substantia Nigra	brain
45	chr17:46061200-46062600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr17:46061200-46063000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr17:46061200-46063800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:46061200-46064000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr17:46061200-46064600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr17:46061200-46064600	Weak transcription	Brain Germinal Matrix	brain

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