Variant report

Variant	rs4902566
Chromosome Location	chr14:68793554-68793555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:68793230..68795249-chr14:68798426..68801112,3	MCF-7	breast:
2	chr14:68778894..68781152-chr14:68792473..68795280,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10083393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10131654	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10135678	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10136039	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10144669	0.95[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10483807	0.90[GIH][hapmap]
rs11158728	1.00[GIH][hapmap]
rs11158730	0.90[GIH][hapmap]
rs11621881	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11627646	1.00[GIH][hapmap]
rs12880109	0.88[GIH][hapmap]
rs12890124	1.00[GIH][hapmap]
rs12892777	0.90[GIH][hapmap]
rs1956523	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1956524	0.81[CHB][hapmap]
rs1956525	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1956526	0.80[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1956528	1.00[GIH][hapmap]
rs1956529	1.00[GIH][hapmap]
rs1956532	1.00[GIH][hapmap]
rs2013413	0.90[GIH][hapmap]
rs2064912	1.00[GIH][hapmap]
rs2064914	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2145422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2145423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3784104	1.00[GIH][hapmap]
rs3784106	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3784108	0.81[CHD][hapmap];1.00[GIH][hapmap]
rs4410007	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4899238	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7147852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7148322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7148412	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7149396	0.94[ASW][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7150988	1.00[GIH][hapmap]
rs7151629	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7493547	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8013078	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8013968	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8017304	1.00[GIH][hapmap]
rs8022860	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs911254	0.90[GIH][hapmap]
rs911255	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs911258	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs927220	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9323506	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9989152	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][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	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
rs4902566	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr14:68783400-68793600	Weak transcription	Pancreas	Pancrea
3	chr14:68785600-68793600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr14:68785600-68812400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr14:68786600-68795200	Weak transcription	Aorta	Aorta
6	chr14:68786600-68799000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr14:68786800-68798800	Weak transcription	Brain Anterior Caudate	brain
8	chr14:68787400-68798400	Weak transcription	Fetal Stomach	stomach
9	chr14:68787600-68795200	Weak transcription	Spleen	Spleen
10	chr14:68788200-68793600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr14:68788200-68807000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr14:68788400-68796600	Weak transcription	Fetal Lung	lung
13	chr14:68789600-68810400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:68790200-68795600	Weak transcription	Psoas Muscle	Psoas
15	chr14:68790400-68795400	Enhancers	Primary B cells from peripheral blood	blood
16	chr14:68790800-68799200	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:68791400-68795000	Enhancers	Primary B cells from cord blood	blood
18	chr14:68792600-68798200	Weak transcription	Fetal Intestine Small	intestine
19	chr14:68793000-68793800	Enhancers	Colon Smooth Muscle	Colon
20	chr14:68793200-68794400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr14:68793200-68794400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr14:68793400-68793600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr14:68793400-68794200	Enhancers	Primary hematopoietic stem cells	blood
24	chr14:68793400-68795000	Enhancers	GM12878-XiMat	blood

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