Variant report

Variant	rs1956526
Chromosome Location	chr14:68799787-68799788
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68797384..68800129-chr14:68809250..68811315,3	MCF-7	breast:
2	chr14:68798605..68800534-chr14:68804811..68807442,2	K562	blood:
3	chr14:68793230..68795249-chr14:68798426..68801112,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240210	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10083393	0.80[ASN][1000 genomes]
rs10131654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10141370	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10144669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1028577	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10483807	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1108590	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11158728	0.92[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs11158729	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11158730	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11621881	0.97[ASN][1000 genomes]
rs11626138	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11626195	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11627646	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11628825	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11628890	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11628954	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12878627	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12878858	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12880109	0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12880842	0.89[EUR][1000 genomes]
rs12881502	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12883719	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12884901	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12885750	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12886238	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12889949	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12890110	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12890124	0.96[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12890167	0.91[EUR][1000 genomes]
rs12892777	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12896939	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1956523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1956524	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1956525	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956528	0.93[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1956529	0.96[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1956532	0.96[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2013413	0.92[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2064911	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2064912	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2145422	0.96[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2145423	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2180769	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2180770	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2877455	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs3784104	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3784106	0.84[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3784108	0.93[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3784109	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3784110	0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3784111	0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs3825730	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4410007	0.99[ASN][1000 genomes]
rs4899238	0.99[ASN][1000 genomes]
rs4902566	0.80[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs61985135	0.91[EUR][1000 genomes]
rs61985136	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62635808	0.84[ASN][1000 genomes]
rs7144422	0.86[ASN][1000 genomes]
rs7146110	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7146850	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7147852	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7148073	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7148322	0.86[JPT][hapmap]
rs7148412	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7149396	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7150988	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7151629	0.95[GIH][hapmap]
rs7155473	0.86[EUR][1000 genomes]
rs7158493	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7493547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8013078	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8013968	0.98[ASN][1000 genomes]
rs8017304	0.96[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8022860	0.99[ASN][1000 genomes]
rs911254	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs911255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs911258	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs927220	0.85[GIH][hapmap]
rs9989152	0.91[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv564962	chr14:68795209-68837882	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1956526	MTHFD1	cis	cerebellum	SCAN
rs1956526	EIF2S1	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 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	chr14:68785600-68812400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr14:68788200-68807000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:68789600-68810400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:68796600-68799800	Enhancers	Fetal Lung	lung
6	chr14:68796800-68800200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr14:68798200-68799800	Enhancers	Fetal Intestine Small	intestine
8	chr14:68798200-68800000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr14:68798200-68800200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr14:68798200-68800200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr14:68798200-68800600	Enhancers	Colon Smooth Muscle	Colon
12	chr14:68798200-68802400	Enhancers	Primary B cells from cord blood	blood
13	chr14:68798400-68799800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr14:68798400-68800000	Enhancers	Fetal Stomach	stomach
15	chr14:68798800-68799800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr14:68799000-68800000	Enhancers	Rectal Smooth Muscle	rectum
17	chr14:68799200-68800000	Enhancers	Fetal Muscle Leg	muscle
18	chr14:68799200-68801600	Enhancers	Primary B cells from peripheral blood	blood
19	chr14:68799200-68802200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:68799400-68804000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr14:68799400-68806400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:68799600-68799800	Flanking Active TSS	GM12878-XiMat	blood
23	chr14:68799600-68800000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:68799600-68800400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr14:68799600-68800800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr14:68799600-68803400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:68799600-68804000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr14:68799600-68806400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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