Variant report

Variant	rs3784121
Chromosome Location	chr14:68883688-68883689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68883175..68885283-chr14:68918450..68920761,2	MCF-7	breast:
2	chr14:68881675..68884365-chr14:69252579..69254360,2	MCF-7	breast:
3	chr14:68863146..68866898-chr14:68882756..68885018,4	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1108007	1.00[JPT][hapmap]
rs11846360	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11847185	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11849916	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468278	0.92[ASN][1000 genomes]
rs17105463	1.00[JPT][hapmap]
rs17105469	1.00[JPT][hapmap]
rs17105515	1.00[JPT][hapmap]
rs17105522	0.81[ASN][1000 genomes]
rs17105667	1.00[YRI][hapmap]
rs17105669	1.00[YRI][hapmap]
rs17105675	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17755657	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17755734	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs17755752	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs17828691	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17828721	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17828763	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1956535	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2107339	1.00[YRI][hapmap]
rs2331705	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs34256824	0.92[ASN][1000 genomes]
rs35190649	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60443209	0.89[AFR][1000 genomes]
rs61064711	0.89[AFR][1000 genomes]
rs7149983	0.92[ASN][1000 genomes]
rs73276281	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73276290	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3784121	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68867200-68886400	Weak transcription	Dnd41	blood
2	chr14:68868200-68887200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:68873400-68883800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:68875000-68883800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:68875000-68883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr14:68875400-68884200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:68877000-68885600	Weak transcription	Primary T cells from cord blood	blood
8	chr14:68877000-68886000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr14:68877200-68890600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:68877400-68885200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr14:68880000-68885000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:68880200-68885000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:68880200-68885000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:68880200-68885000	Weak transcription	NHEK	skin
15	chr14:68880400-68884200	Enhancers	Colon Smooth Muscle	Colon
16	chr14:68880400-68885000	Weak transcription	HMEC	breast
17	chr14:68880600-68884200	Enhancers	Fetal Stomach	stomach
18	chr14:68880800-68885800	Enhancers	Fetal Lung	lung
19	chr14:68881000-68886400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:68881000-68890600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr14:68881400-68887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr14:68881800-68884200	Enhancers	Stomach Smooth Muscle	stomach
23	chr14:68881800-68886000	Enhancers	Fetal Muscle Leg	muscle
24	chr14:68882200-68884400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr14:68882200-68890000	Weak transcription	Small Intestine	intestine
26	chr14:68882400-68893400	Weak transcription	Fetal Intestine Small	intestine
27	chr14:68882800-68884000	Enhancers	Primary B cells from cord blood	blood
28	chr14:68883000-68886000	Enhancers	Fetal Kidney	kidney
29	chr14:68883200-68886200	Weak transcription	Fetal Thymus	thymus
30	chr14:68883400-68884400	Enhancers	Ovary	ovary
31	chr14:68883400-68884600	Enhancers	Esophagus	oesophagus
32	chr14:68883400-68885000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:68883400-68888200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr14:68883600-68884000	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links