Variant report

Variant	rs2256191
Chromosome Location	chr14:64656855-64656856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10162323	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1152590	0.84[CEU][hapmap];0.90[MEX][hapmap]
rs1152592	0.88[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs1152594	0.84[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs1152601	0.86[CEU][hapmap]
rs12435376	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255990	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs1255991	0.80[EUR][1000 genomes]
rs1262242	0.82[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1272715	0.81[EUR][1000 genomes]
rs1953234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2027094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2776607	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2781380	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987983	0.89[MEX][hapmap]
rs6573547	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573548	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148072	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148637	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs872227	0.82[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs968257	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv902021	chr14:64647646-64715794	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2256191	MTHFD1	cis	parietal	SCAN
rs2256191	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs2256191	MTHFD1	cis	cerebellum	SCAN
rs2256191	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs2256191	KCNH5	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64625000-64658000	Weak transcription	HUVEC	blood vessel
3	chr14:64627200-64660400	Weak transcription	Fetal Heart	heart
4	chr14:64636400-64658400	Weak transcription	HMEC	breast
5	chr14:64636800-64662600	Weak transcription	Psoas Muscle	Psoas
6	chr14:64637400-64663600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:64639200-64658000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:64640000-64663400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr14:64640200-64658000	Weak transcription	NHEK	skin
10	chr14:64644600-64658800	Weak transcription	NHLF	lung
11	chr14:64645200-64661000	Weak transcription	Primary B cells from cord blood	blood
12	chr14:64645800-64661400	Weak transcription	Small Intestine	intestine
13	chr14:64645800-64663600	Weak transcription	Colonic Mucosa	Colon
14	chr14:64650400-64660000	Strong transcription	Aorta	Aorta
15	chr14:64650400-64660000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr14:64650400-64660200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr14:64650400-64660600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr14:64650800-64658200	Strong transcription	Placenta	Placenta
19	chr14:64650800-64659800	Strong transcription	Left Ventricle	heart
20	chr14:64650800-64661400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr14:64650800-64661600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:64650800-64663200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr14:64650800-64671800	Strong transcription	Liver	Liver
24	chr14:64651000-64660400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr14:64651400-64659400	Weak transcription	Right Ventricle	heart
26	chr14:64651600-64657400	Strong transcription	GM12878-XiMat	blood
27	chr14:64651600-64662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:64651800-64661000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:64652000-64658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:64652000-64661400	Weak transcription	Fetal Kidney	kidney
31	chr14:64652000-64662800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:64652600-64658000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:64652800-64658000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr14:64652800-64659000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr14:64652800-64660000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr14:64652800-64666200	Strong transcription	Dnd41	blood
37	chr14:64653000-64658200	Strong transcription	Esophagus	oesophagus
38	chr14:64653000-64658600	Strong transcription	Lung	lung
39	chr14:64653000-64659800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:64653000-64660000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr14:64653000-64660000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr14:64653000-64660400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:64653000-64660800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr14:64653000-64661200	Strong transcription	Fetal Intestine Large	intestine
45	chr14:64653000-64664000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr14:64653200-64657600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr14:64653200-64657800	Strong transcription	Fetal Brain Female	brain
48	chr14:64653200-64660000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:64653200-64660000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr14:64653600-64661200	Weak transcription	Gastric	stomach

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