Variant report

Variant	rs13101987
Chromosome Location	chr4:78678515-78678516
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78676799..78679930-chr4:78739858..78742459,3	K562	blood:
2	chr4:78676527..78678706-chr4:78694641..78697046,2	K562	blood:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10033527	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10033613	0.84[ASN][1000 genomes]
rs11097938	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs11728886	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729215	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13101418	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs13103035	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13103523	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13104947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13106067	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13120272	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16996915	0.82[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134050	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34830788	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35735677	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4453957	0.84[ASN][1000 genomes]
rs4577601	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs4859509	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4859511	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4859875	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859877	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859879	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859889	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap]
rs6533282	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs6533291	0.84[ASN][1000 genomes]
rs6533344	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6814912	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6854895	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7670157	0.82[ASW][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.96[MKK][hapmap]
rs7675009	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs7698627	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[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	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13101987	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs13101987	MRPL1	cis	parietal	SCAN
rs13101987	MRPL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
2	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
3	chr4:78643800-78714000	Weak transcription	Lung	lung
4	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
6	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
7	chr4:78650200-78697800	Weak transcription	Gastric	stomach
8	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
11	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
13	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
14	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
15	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
16	chr4:78662000-78695600	Weak transcription	Ovary	ovary
17	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
18	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
19	chr4:78662200-78682400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:78662600-78679800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:78662800-78683400	Weak transcription	Fetal Kidney	kidney
23	chr4:78662800-78683600	Weak transcription	K562	blood
24	chr4:78663800-78695600	Weak transcription	Left Ventricle	heart
25	chr4:78665200-78682200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:78667200-78682600	Weak transcription	HepG2	liver
27	chr4:78673200-78678800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:78673200-78680000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:78673400-78679200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:78673400-78679400	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:78673400-78679600	Weak transcription	Thymus	Thymus
32	chr4:78673400-78681000	Weak transcription	Fetal Intestine Large	intestine
33	chr4:78673400-78682600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:78673400-78687000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:78673400-78692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:78673600-78680000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:78673600-78682200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:78673600-78682400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:78673600-78682400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:78674400-78679000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:78674600-78679600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:78674800-78679800	Weak transcription	Fetal Brain Female	brain
43	chr4:78675800-78679600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:78676000-78678600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:78676000-78681400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:78676200-78679000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:78676200-78679200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:78676200-78679400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:78676200-78681800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:78676200-78682400	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links