Variant report

Variant	rs3207348
Chromosome Location	chr11:93212245-93212246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11020387	0.80[EUR][1000 genomes]
rs11020388	0.80[EUR][1000 genomes]
rs11020390	0.80[EUR][1000 genomes]
rs11603107	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603540	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603560	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11604399	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606253	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606261	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606262	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606505	0.80[EUR][1000 genomes]
rs11607585	0.80[EUR][1000 genomes]
rs12791489	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12796609	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12797006	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12806700	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12808363	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808921	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2605596	0.91[ASN][1000 genomes]
rs2658797	0.91[ASN][1000 genomes]
rs28638787	0.80[EUR][1000 genomes]
rs34028949	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34580908	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34716358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34819559	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34825570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35061570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364744	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35368196	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35548120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901746	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35930354	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794007	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794008	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6483248	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66464546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67927069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111773	0.80[EUR][1000 genomes]
rs7130465	0.80[EUR][1000 genomes]
rs71480681	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71480682	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7365	0.83[ASN][1000 genomes]
rs7928401	0.80[EUR][1000 genomes]
rs897555	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3207348	SMCO4	cis	Whole Blood	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93200600-93214400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:93207000-93239000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:93207800-93220000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:93208200-93223200	Weak transcription	GM12878-XiMat	blood
5	chr11:93208400-93218400	Weak transcription	Left Ventricle	heart
6	chr11:93208600-93217800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:93208800-93213000	Strong transcription	Liver	Liver
8	chr11:93209000-93214200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:93209000-93231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:93209000-93235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:93209200-93213200	Weak transcription	Small Intestine	intestine
12	chr11:93209200-93215000	Weak transcription	Right Ventricle	heart
13	chr11:93209200-93229200	Weak transcription	Dnd41	blood
14	chr11:93209400-93214200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:93209400-93215000	Weak transcription	Right Atrium	heart
16	chr11:93209400-93218800	Strong transcription	Fetal Intestine Small	intestine
17	chr11:93209600-93213000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr11:93209600-93214800	Strong transcription	Aorta	Aorta
19	chr11:93209600-93229400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr11:93209800-93213000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:93209800-93217200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:93210000-93215800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr11:93210200-93212600	Enhancers	Fetal Brain Male	brain
24	chr11:93210400-93213000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr11:93210400-93213800	Weak transcription	Stomach Mucosa	stomach
26	chr11:93210600-93213000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:93210600-93213200	Strong transcription	Lung	lung
28	chr11:93210600-93214400	Weak transcription	Esophagus	oesophagus
29	chr11:93210600-93214800	Strong transcription	Spleen	Spleen
30	chr11:93210600-93215400	Weak transcription	Fetal Lung	lung
31	chr11:93210600-93220000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:93210600-93231600	Weak transcription	A549	lung
33	chr11:93210800-93212400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:93210800-93213400	Strong transcription	Pancreas	Pancrea
35	chr11:93211000-93212400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr11:93211000-93214200	Weak transcription	Fetal Muscle Leg	muscle
37	chr11:93211000-93214200	Weak transcription	Hela-S3	cervix
38	chr11:93211000-93218600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:93211000-93225800	Weak transcription	Thymus	Thymus
40	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
41	chr11:93211200-93215600	Weak transcription	Fetal Brain Female	brain
42	chr11:93211200-93222000	Weak transcription	Adipose Nuclei	Adipose
43	chr11:93211400-93213000	Strong transcription	Fetal Intestine Large	intestine
44	chr11:93211600-93212400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr11:93211600-93212400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:93211600-93212800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr11:93211600-93213000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr11:93211600-93215000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:93211600-93215000	Strong transcription	Fetal Stomach	stomach
50	chr11:93211600-93216600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links