Variant report

Variant	rs11627646
Chromosome Location	chr14:68809564-68809565
allele	A/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	chr14:68808236..68811175-chr14:68815933..68818264,2	K562	blood:
3	chr14:68808236..68810684-chr14:68816764..68819058,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10141370	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1028577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10483807	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1108590	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158728	0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs11158729	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158730	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11626138	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11626195	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11628825	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11628890	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11628954	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12878627	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12878858	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12880109	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12880842	0.92[EUR][1000 genomes]
rs12881502	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12883719	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs12884901	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885750	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12886238	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12889949	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12890110	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12890124	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]
rs12890167	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12892777	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12896939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1956524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956525	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1956526	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]
rs1956528	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1956529	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]
rs1956532	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013413	0.91[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2064911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145422	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2145423	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2180769	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2180770	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2877455	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784104	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784106	0.88[GIH][hapmap]
rs3784108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784109	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825730	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902562	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs4902566	1.00[GIH][hapmap]
rs61985135	0.92[EUR][1000 genomes]
rs61985136	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6573823	1.00[YRI][hapmap]
rs7146850	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7147852	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7148073	0.92[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7149396	0.85[GIH][hapmap]
rs7150988	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][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]
rs7151629	0.90[GIH][hapmap]
rs7155473	0.88[EUR][1000 genomes]
rs7158493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017304	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs911254	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs927220	1.00[GIH][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11627646	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

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	chr14:68789600-68810400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:68804000-68810400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:68804000-68813400	Weak transcription	Colon Smooth Muscle	Colon
6	chr14:68804400-68812800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr14:68806200-68811200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:68806400-68810800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr14:68806400-68810800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr14:68806400-68810800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr14:68806400-68811000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr14:68806600-68809600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr14:68806800-68809600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr14:68807000-68809600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr14:68807000-68811000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr14:68807000-68811000	Enhancers	Primary B cells from peripheral blood	blood
17	chr14:68807200-68810600	Weak transcription	Gastric	stomach
18	chr14:68807600-68811000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr14:68807800-68810000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr14:68808200-68809600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr14:68808200-68809600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:68808200-68809600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr14:68808200-68811000	Enhancers	Primary T cells from cord blood	blood
24	chr14:68808200-68811000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr14:68808200-68811200	Enhancers	Fetal Thymus	thymus
26	chr14:68808400-68809600	Enhancers	Duodenum Mucosa	Duodenum
27	chr14:68808600-68810400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr14:68808600-68812200	Weak transcription	Fetal Muscle Leg	muscle
29	chr14:68808600-68819200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr14:68808800-68809600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr14:68808800-68810000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr14:68808800-68811000	Enhancers	Thymus	Thymus
33	chr14:68808800-68812200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:68808800-68813000	Weak transcription	Brain Anterior Caudate	brain
35	chr14:68808800-68813000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr14:68809000-68809600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr14:68809000-68809600	Enhancers	K562	blood
38	chr14:68809000-68810200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr14:68809000-68810400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr14:68809000-68816400	Weak transcription	Fetal Intestine Large	intestine
41	chr14:68809200-68810200	Weak transcription	Fetal Lung	lung
42	chr14:68809200-68810400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr14:68809200-68811000	Enhancers	GM12878-XiMat	blood
44	chr14:68809200-68812000	Weak transcription	Fetal Intestine Small	intestine
45	chr14:68809200-68812200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr14:68809200-68813200	Weak transcription	Small Intestine	intestine
47	chr14:68809400-68809800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr14:68809400-68810400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr14:68809400-68810600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr14:68809400-68810600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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