Variant report

Variant	rs1108301
Chromosome Location	chr3:47029426-47029427
allele	A/G
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	chr3:47028290..47030861-chr3:47204654..47207061,2	K562	blood:
2	chr3:46943427..46945149-chr3:47026537..47029447,2	K562	blood:
3	chr3:46967003..46969094-chr3:47027907..47030796,2	K562	blood:
4	chr3:46949254..46951552-chr3:47027591..47030154,3	K562	blood:
5	chr3:46974856..46983636-chr3:47025231..47032249,9	K562	blood:
6	chr3:46987136..46991583-chr3:47027983..47031367,6	K562	blood:
7	chr3:47028266..47031256-chr3:47034300..47036067,3	MCF-7	breast:
8	chr3:46967003..46969518-chr3:47029296..47031281,2	K562	blood:
9	chr3:46949955..46951552-chr3:47027591..47029507,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000227398	Chromatin interaction
ENSG00000160801	Chromatin interaction
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10433549	0.87[EUR][1000 genomes]
rs10461018	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1079276	0.96[EUR][1000 genomes]
rs11130110	0.96[EUR][1000 genomes]
rs11130111	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11130112	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707736	0.80[EUR][1000 genomes]
rs11709660	0.81[EUR][1000 genomes]
rs11715121	0.81[EUR][1000 genomes]
rs11716553	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11720139	0.88[EUR][1000 genomes]
rs11917361	0.83[EUR][1000 genomes]
rs11917474	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12152493	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491473	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12630534	0.96[EUR][1000 genomes]
rs12715421	0.82[EUR][1000 genomes]
rs13062681	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13066214	0.96[EUR][1000 genomes]
rs13077398	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13091054	0.87[EUR][1000 genomes]
rs1463393	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17784127	0.85[EUR][1000 genomes]
rs1869869	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1869871	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061197	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2278963	0.88[EUR][1000 genomes]
rs2305634	0.96[EUR][1000 genomes]
rs2305635	0.88[EUR][1000 genomes]
rs2305638	0.91[EUR][1000 genomes]
rs2385867	0.93[EUR][1000 genomes]
rs34103310	0.89[EUR][1000 genomes]
rs34344887	0.95[EUR][1000 genomes]
rs4078466	0.85[EUR][1000 genomes]
rs4082155	0.85[EUR][1000 genomes]
rs4234465	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682831	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682837	0.96[EUR][1000 genomes]
rs4682844	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683322	0.81[EUR][1000 genomes]
rs55724164	0.83[EUR][1000 genomes]
rs55843455	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927279	0.82[EUR][1000 genomes]
rs56217494	0.85[EUR][1000 genomes]
rs56249396	0.83[EUR][1000 genomes]
rs61729713	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62246375	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62246398	0.83[EUR][1000 genomes]
rs62248439	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6442055	0.81[EUR][1000 genomes]
rs66539935	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66564457	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6763236	0.88[EUR][1000 genomes]
rs6767218	0.83[EUR][1000 genomes]
rs6768722	0.81[EUR][1000 genomes]
rs6774733	0.96[EUR][1000 genomes]
rs6777145	0.81[EUR][1000 genomes]
rs6794193	0.87[EUR][1000 genomes]
rs6808742	0.91[EUR][1000 genomes]
rs749511	0.88[EUR][1000 genomes]
rs7610636	0.92[EUR][1000 genomes]
rs7617689	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7625067	0.89[EUR][1000 genomes]
rs7625070	0.89[EUR][1000 genomes]
rs7628747	0.96[EUR][1000 genomes]
rs7633698	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7636252	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7637302	0.86[EUR][1000 genomes]
rs7640397	0.96[EUR][1000 genomes]
rs9844122	0.80[EUR][1000 genomes]
rs9845728	0.80[EUR][1000 genomes]
rs9854790	0.81[EUR][1000 genomes]
rs9858443	0.82[EUR][1000 genomes]
rs9875235	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1108301	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs1108301	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47021800-47036000	Weak transcription	Ovary	ovary
2	chr3:47022000-47030200	Weak transcription	Aorta	Aorta
3	chr3:47022200-47030200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:47022400-47029600	Weak transcription	Liver	Liver
5	chr3:47022400-47039800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
9	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
10	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:47023600-47035600	Weak transcription	Brain Anterior Caudate	brain
13	chr3:47023800-47029600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:47024200-47030400	Weak transcription	Fetal Brain Female	brain
15	chr3:47024400-47030000	Enhancers	Stomach Mucosa	stomach
16	chr3:47024400-47039600	Weak transcription	HepG2	liver
17	chr3:47024600-47031800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:47025800-47031800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:47026000-47029800	Genic enhancers	Fetal Intestine Small	intestine
20	chr3:47026200-47029800	Enhancers	Lung	lung
21	chr3:47026200-47030000	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:47026200-47030200	Enhancers	Gastric	stomach
23	chr3:47026600-47029600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:47026600-47029800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:47026600-47030000	Enhancers	Right Ventricle	heart
26	chr3:47026600-47033200	Enhancers	Placenta	Placenta
27	chr3:47026800-47031000	Enhancers	Left Ventricle	heart
28	chr3:47027000-47030200	Enhancers	Spleen	Spleen
29	chr3:47027000-47032000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:47027200-47029600	Enhancers	HMEC	breast
31	chr3:47027200-47029800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:47027600-47030200	Enhancers	A549	lung
33	chr3:47028000-47029800	Enhancers	Fetal Muscle Leg	muscle
34	chr3:47028000-47030200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:47028000-47032000	Enhancers	HUVEC	blood vessel
36	chr3:47028200-47029600	Flanking Active TSS	Fetal Thymus	thymus
37	chr3:47028200-47029600	Flanking Active TSS	Dnd41	blood
38	chr3:47028200-47030200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr3:47028200-47030400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr3:47028200-47030600	Enhancers	Fetal Muscle Trunk	muscle
41	chr3:47028400-47029800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:47028400-47029800	Enhancers	Small Intestine	intestine
43	chr3:47028400-47030000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:47028400-47030000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:47028400-47030000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr3:47028400-47030200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:47028400-47030200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr3:47028400-47030200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:47028400-47030400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr3:47028400-47030400	Flanking Active TSS	GM12878-XiMat	blood

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