Variant report

Variant	rs11158728
Chromosome Location	chr14:68762205-68762206
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68750225..68753988-chr14:68760767..68763895,3	K562	blood:
2	chr14:68760176..68762768-chr14:69258282..69260284,2	MCF-7	breast:
3	chr14:68729921..68731591-chr14:68760748..68763358,2	MCF-7	breast:
4	chr14:68760897..68764007-chr14:68767297..68769142,3	K562	blood:
5	chr14:68762186..68763785-chr14:68835933..68838627,2	K562	blood:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10141370	0.96[EUR][1000 genomes]
rs1028577	0.90[EUR][1000 genomes]
rs10483807	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1108590	0.97[EUR][1000 genomes]
rs11158729	0.97[EUR][1000 genomes]
rs11158730	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11626138	0.96[EUR][1000 genomes]
rs11626195	0.97[EUR][1000 genomes]
rs11627646	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs11628825	0.97[EUR][1000 genomes]
rs11628890	0.96[EUR][1000 genomes]
rs11628954	0.97[EUR][1000 genomes]
rs12878627	0.96[EUR][1000 genomes]
rs12878858	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs12880109	0.96[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12880842	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12881502	0.96[EUR][1000 genomes]
rs12883719	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12884901	0.95[EUR][1000 genomes]
rs12885750	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs12886238	0.96[EUR][1000 genomes]
rs12889949	0.97[EUR][1000 genomes]
rs12890110	0.98[EUR][1000 genomes]
rs12890124	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs12890167	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12892777	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs12896939	0.92[EUR][1000 genomes]
rs1956524	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs1956525	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs1956526	0.92[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1956528	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1956529	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1956532	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2013413	0.92[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2064911	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2064912	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2145422	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs2145423	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2180769	0.94[EUR][1000 genomes]
rs2180770	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs2877455	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3784104	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs3784106	0.88[GIH][hapmap]
rs3784108	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs3784109	0.96[EUR][1000 genomes]
rs3825730	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs4902566	1.00[GIH][hapmap]
rs61985135	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61985136	0.97[EUR][1000 genomes]
rs7146850	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs7147852	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7148073	0.88[CEU][hapmap];0.96[EUR][1000 genomes]
rs7149396	0.85[GIH][hapmap]
rs7150988	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7151629	0.90[GIH][hapmap]
rs7155473	0.95[EUR][1000 genomes]
rs7158493	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs8017304	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs911254	0.96[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs927220	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv428628	chr14:68674504-68835127	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11158728	MTHFD1	cis	cerebellum	SCAN
rs11158728	C14orf181	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68746600-68764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:68752400-68765000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:68752400-68768800	Weak transcription	Aorta	Aorta
4	chr14:68752600-68763800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr14:68753400-68768800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:68753600-68768600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:68753600-68768800	Weak transcription	Dnd41	blood
8	chr14:68756400-68763400	Enhancers	Primary B cells from peripheral blood	blood
9	chr14:68756600-68765200	Enhancers	Fetal Intestine Small	intestine
10	chr14:68757800-68765200	Enhancers	Fetal Intestine Large	intestine
11	chr14:68758200-68762800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr14:68758200-68762800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr14:68758200-68762800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr14:68758200-68763000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr14:68758200-68763000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr14:68758200-68765600	Enhancers	Primary T cells from cord blood	blood
17	chr14:68758400-68762400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:68758400-68762600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr14:68758400-68762600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:68758400-68763600	Enhancers	Colon Smooth Muscle	Colon
21	chr14:68758400-68765600	Enhancers	Fetal Kidney	kidney
22	chr14:68758400-68765600	Enhancers	Fetal Muscle Leg	muscle
23	chr14:68758600-68765200	Enhancers	Fetal Lung	lung
24	chr14:68759000-68768400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr14:68759600-68762800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:68759600-68763400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:68760000-68768800	Weak transcription	Thymus	Thymus
28	chr14:68760200-68763600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:68760400-68762400	Weak transcription	Right Atrium	heart
30	chr14:68760400-68762800	Enhancers	Primary B cells from cord blood	blood
31	chr14:68760400-68768800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr14:68760400-68776800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:68760600-68763200	Weak transcription	Adipose Nuclei	Adipose
34	chr14:68760600-68763400	Enhancers	Fetal Heart	heart
35	chr14:68760600-68764800	Weak transcription	HUVEC	blood vessel
36	chr14:68760600-68765000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:68760600-68768400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr14:68760600-68768600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:68760600-68773600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr14:68760800-68762800	Enhancers	GM12878-XiMat	blood
41	chr14:68761000-68762400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr14:68761000-68765200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr14:68761000-68767600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:68761200-68762400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr14:68761200-68762400	Enhancers	Stomach Mucosa	stomach
46	chr14:68761200-68763000	Enhancers	Duodenum Mucosa	Duodenum
47	chr14:68761200-68763400	Enhancers	Pancreas	Pancrea
48	chr14:68761200-68765200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr14:68761400-68765200	Enhancers	Ovary	ovary
50	chr14:68761600-68762400	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links