Variant report

Variant	rs7140695
Chromosome Location	chr14:65929132-65929133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10138671	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs10142283	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[EUR][1000 genomes]
rs10143206	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs10144979	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10145146	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10148529	0.92[EUR][1000 genomes]
rs10150412	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10152007	0.96[CEU][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs10873190	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10873191	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1113962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11158595	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158597	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11158603	0.96[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11158604	0.93[EUR][1000 genomes]
rs11158605	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11158607	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11623662	0.84[CEU][hapmap]
rs11629437	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11844682	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11848209	1.00[YRI][hapmap]
rs12433597	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12587057	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12885842	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889731	0.81[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1953415	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1953418	0.96[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1958559	0.81[CEU][hapmap]
rs1958560	0.81[CEU][hapmap]
rs1959144	0.81[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1959145	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1999725	0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs2064695	0.81[CEU][hapmap]
rs2092914	0.92[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2149839	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2152374	0.82[EUR][1000 genomes]
rs2183277	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2184601	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2185454	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2210805	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2268955	0.81[CEU][hapmap]
rs2268956	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2300864	0.88[EUR][1000 genomes]
rs2411354	0.95[YRI][hapmap]
rs2411356	0.84[CEU][hapmap];0.85[YRI][hapmap]
rs2411815	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2411820	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2411823	0.89[CEU][hapmap]
rs2898814	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2898816	1.00[YRI][hapmap]
rs2898818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898820	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3825639	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4587890	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs4902399	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4902404	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902408	1.00[YRI][hapmap]
rs61987993	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6573612	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6573614	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6573615	0.84[CEU][hapmap]
rs6573616	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6573617	0.83[EUR][1000 genomes]
rs6573618	0.93[EUR][1000 genomes]
rs6573619	0.84[YRI][hapmap];0.92[EUR][1000 genomes]
rs7140341	0.96[CEU][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7141367	1.00[YRI][hapmap]
rs7141536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7142906	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7143318	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7144345	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs7144415	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7144971	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs7145500	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs7145759	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[EUR][1000 genomes]
rs7146993	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7147002	0.96[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7147536	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap]
rs7147636	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs7150094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7150448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7150648	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7151561	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7157109	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7158153	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7160390	1.00[YRI][hapmap]
rs7160780	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs8003464	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8005243	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8007497	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs8010726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8011224	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8012834	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8013442	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8017880	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8019762	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs8022053	0.85[EUR][1000 genomes]
rs8022080	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9323460	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9323461	0.96[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9972106	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7140695	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65892800-65929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr14:65898400-65935600	Weak transcription	Gastric	stomach
3	chr14:65905800-65936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:65911200-65942400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr14:65913800-65942400	Weak transcription	Left Ventricle	heart
6	chr14:65917200-65936600	Weak transcription	Pancreas	Pancrea
7	chr14:65918600-65935600	Weak transcription	Fetal Stomach	stomach
8	chr14:65920400-65937800	Weak transcription	Ovary	ovary
9	chr14:65920800-65942400	Weak transcription	Stomach Mucosa	stomach
10	chr14:65922200-65936400	Weak transcription	Placenta	Placenta
11	chr14:65923200-65934800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr14:65923200-65936000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:65923200-65938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr14:65923400-65935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:65923400-65937000	Weak transcription	Brain Germinal Matrix	brain
16	chr14:65923400-65938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:65923400-65945000	Weak transcription	NHDF-Ad	bronchial
18	chr14:65924000-65937600	Weak transcription	Fetal Brain Female	brain
19	chr14:65924200-65936600	Weak transcription	Lung	lung
20	chr14:65924400-65930200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:65924400-65935400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr14:65924600-65935400	Weak transcription	Fetal Intestine Small	intestine
23	chr14:65925200-65936000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr14:65925600-65931600	Strong transcription	Dnd41	blood
25	chr14:65925800-65943200	Weak transcription	Thymus	Thymus
26	chr14:65926000-65938200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:65927000-65929200	Enhancers	Brain Substantia Nigra	brain
28	chr14:65927200-65929400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr14:65927400-65930400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:65927600-65929200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:65927600-65934800	Weak transcription	Fetal Lung	lung
32	chr14:65927600-65935400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:65927600-65936600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:65927600-65936600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:65927800-65929200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr14:65927800-65929200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr14:65927800-65929800	Enhancers	HMEC	breast
38	chr14:65928000-65929200	Genic enhancers	Primary B cells from cord blood	blood
39	chr14:65928000-65929200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr14:65928000-65929200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr14:65928000-65929200	Enhancers	Brain Anterior Caudate	brain
42	chr14:65928000-65929200	Enhancers	NHEK	skin
43	chr14:65928000-65929400	Enhancers	Brain Angular Gyrus	brain
44	chr14:65928000-65929800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr14:65928000-65929800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr14:65928000-65929800	Flanking Active TSS	GM12878-XiMat	blood
47	chr14:65928000-65929800	Enhancers	Osteobl	bone
48	chr14:65928000-65930200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr14:65928000-65930400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr14:65928000-65936200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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