Variant report

Variant	rs1956529
Chromosome Location	chr14:68788924-68788925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:68782864..68784821-chr14:68788209..68789898,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10141370	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1028577	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10483807	0.91[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1108590	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158728	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs11158729	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158730	0.91[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11626138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626195	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11628825	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11628954	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12878627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878858	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12880109	0.91[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12880842	0.95[EUR][1000 genomes]
rs12881502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883719	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12884901	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12885750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12886238	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12889949	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12890110	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12890124	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]
rs12890167	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12892777	1.00[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12896939	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1956524	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956525	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1956526	0.96[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1956528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956532	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013413	0.91[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2064911	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064912	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145422	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2145423	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2180769	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2180770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2877455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825730	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4902562	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs4902566	1.00[GIH][hapmap]
rs61985135	0.95[EUR][1000 genomes]
rs61985136	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6573823	1.00[YRI][hapmap]
rs7146850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147852	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7148073	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7149396	0.85[GIH][hapmap]
rs7150988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151629	0.90[GIH][hapmap]
rs7155473	0.91[EUR][1000 genomes]
rs7158493	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8017304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911254	0.91[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][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

Variant related diseases (count:1)

Disease	PMID	Source
Primary tooth development (number of teeth)	20195514	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1956529	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr14:68776200-68789400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:68777000-68792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:68777000-68793400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr14:68781200-68789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:68783400-68793600	Weak transcription	Pancreas	Pancrea
7	chr14:68784400-68789200	Weak transcription	HepG2	liver
8	chr14:68785600-68789400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:68785600-68793600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr14:68785600-68812400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr14:68786000-68789400	Weak transcription	Psoas Muscle	Psoas
12	chr14:68786400-68789800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:68786600-68789200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:68786600-68795200	Weak transcription	Aorta	Aorta
15	chr14:68786600-68799000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr14:68786800-68789000	Weak transcription	Brain Substantia Nigra	brain
17	chr14:68786800-68798800	Weak transcription	Brain Anterior Caudate	brain
18	chr14:68787000-68792400	Weak transcription	Colon Smooth Muscle	Colon
19	chr14:68787400-68798400	Weak transcription	Fetal Stomach	stomach
20	chr14:68787600-68795200	Weak transcription	Spleen	Spleen
21	chr14:68787800-68791800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr14:68788000-68791400	Weak transcription	Primary B cells from cord blood	blood
23	chr14:68788200-68789200	Weak transcription	Ovary	ovary
24	chr14:68788200-68789400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr14:68788200-68791400	Weak transcription	GM12878-XiMat	blood
26	chr14:68788200-68793600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr14:68788200-68807000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr14:68788400-68789400	Weak transcription	Fetal Muscle Leg	muscle
29	chr14:68788400-68790400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr14:68788400-68796600	Weak transcription	Fetal Lung	lung
31	chr14:68788800-68789800	Weak transcription	Lung	lung

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