Variant report

Variant	rs12890124
Chromosome Location	chr14:68781614-68781615
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	chr14:68771546..68782546-chr14:69251132..69265678,35	MCF-7	breast:
2	chr14:68780053..68783050-chr14:68784750..68787033,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10141370	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1028577	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10483807	1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1108590	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158728	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs11158729	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158730	1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11626138	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11626195	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11627646	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11628825	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11628890	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11628954	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12878627	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12878858	1.00[CEU][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12880109	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12880842	0.97[EUR][1000 genomes]
rs12881502	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12883719	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12884901	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12885750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12886238	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12889949	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12890110	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890167	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12892777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12896939	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1956524	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1956525	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1956526	0.96[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1956528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013413	0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2064911	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064912	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2145422	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2145423	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2180769	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2180770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2877455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784106	0.88[GIH][hapmap]
rs3784108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784109	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825730	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4902566	1.00[GIH][hapmap]
rs61985135	0.97[EUR][1000 genomes]
rs61985136	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7146850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7147852	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7148073	0.92[CEU][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7149396	0.85[GIH][hapmap]
rs7150988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7151629	0.90[GIH][hapmap]
rs7155473	0.93[EUR][1000 genomes]
rs7158493	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8017304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs911254	1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12890124	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68769000-68810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:68772000-68788400	Enhancers	Primary B cells from peripheral blood	blood
3	chr14:68772600-68788000	Weak transcription	Lung	lung
4	chr14:68774400-68785200	Weak transcription	Psoas Muscle	Psoas
5	chr14:68776200-68781800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr14:68776200-68789400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr14:68776400-68785400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:68777000-68781800	Weak transcription	Small Intestine	intestine
9	chr14:68777000-68785800	Weak transcription	Colon Smooth Muscle	Colon
10	chr14:68777000-68792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:68777000-68793400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr14:68777800-68785400	Weak transcription	Fetal Kidney	kidney
13	chr14:68778800-68782000	Enhancers	Primary B cells from cord blood	blood
14	chr14:68779000-68787400	Weak transcription	Primary T cells from cord blood	blood
15	chr14:68779200-68782200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr14:68779400-68781800	Weak transcription	HepG2	liver
17	chr14:68779600-68782200	Enhancers	Fetal Muscle Leg	muscle
18	chr14:68779600-68782800	Weak transcription	Liver	Liver
19	chr14:68780200-68784800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:68780400-68781800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr14:68780400-68785200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:68780400-68785200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr14:68780400-68785400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr14:68780600-68782200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:68780600-68784800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr14:68780600-68785200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:68780800-68782200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:68780800-68783000	Weak transcription	Pancreas	Pancrea
29	chr14:68780800-68787600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr14:68781000-68786200	Weak transcription	Fetal Stomach	stomach
31	chr14:68781200-68781800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr14:68781200-68783200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr14:68781200-68783200	Weak transcription	Ovary	ovary
34	chr14:68781200-68784800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr14:68781200-68785800	Weak transcription	Brain Anterior Caudate	brain
36	chr14:68781200-68786800	Weak transcription	Spleen	Spleen
37	chr14:68781200-68789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:68781400-68781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:68781400-68785200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr14:68781400-68785400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:68781600-68781800	Enhancers	Fetal Lung	lung
42	chr14:68781600-68781800	Enhancers	GM12878-XiMat	blood
43	chr14:68781600-68784200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr14:68781600-68786200	Weak transcription	Brain Substantia Nigra	brain
45	chr14:68781600-68787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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