Variant report

Variant	rs12197795
Chromosome Location	chr6:149293508-149293509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:148899079..148899959-chr6:149293410..149294434,3	MCF-7	breast:
2	chr6:149292734..149295648-chr6:149301183..149303035,2	MCF-7	breast:
3	chr6:149291179..149293538-chr6:149298228..149299764,2	K562	blood:
4	chr6:149066922..149069448-chr6:149293220..149295157,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111962	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12194615	0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12202149	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12204964	0.93[ASW][hapmap];0.85[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12207855	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12207913	0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1384310	0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs1564601	0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1564602	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2340749	0.92[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734376	0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3734377	0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3734378	0.84[ASN][1000 genomes]
rs4358650	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6570918	0.83[ASN][1000 genomes]
rs6924147	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6932862	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6933251	0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6936508	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9322162	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377181	1.00[JPT][hapmap]
rs9377183	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377186	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9386241	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390646	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9404010	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404011	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12197795	MTHFD1L	cis	cerebellum	SCAN
rs12197795	LATS1	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149274000-149293800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:149276400-149308400	Weak transcription	Lung	lung
3	chr6:149278000-149310600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:149284600-149293600	Weak transcription	Esophagus	oesophagus
5	chr6:149284600-149293600	Weak transcription	Ovary	ovary
6	chr6:149286600-149300000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:149286800-149320600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:149288000-149295200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:149288200-149294200	Enhancers	Fetal Muscle Leg	muscle
10	chr6:149289200-149314600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:149290400-149294000	Enhancers	Fetal Muscle Trunk	muscle
12	chr6:149290800-149294000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:149290800-149297200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:149290800-149300400	Weak transcription	Fetal Lung	lung
15	chr6:149290800-149311800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:149291400-149304200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:149291600-149294200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:149292000-149293600	Weak transcription	Right Atrium	heart
19	chr6:149292000-149294000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:149292000-149294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:149292000-149294800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:149292200-149293600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:149292200-149294000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:149292200-149295800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:149292400-149294600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:149292400-149296000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:149292600-149293600	Enhancers	Colonic Mucosa	Colon
28	chr6:149292600-149293800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:149292600-149293800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:149292600-149294000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr6:149292600-149294000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr6:149292600-149294200	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:149292600-149294200	Enhancers	Fetal Thymus	thymus
34	chr6:149292600-149295000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr6:149292800-149294200	Enhancers	Thymus	Thymus
36	chr6:149292800-149294400	Enhancers	Primary B cells from cord blood	blood
37	chr6:149292800-149294600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:149292800-149300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:149292800-149301800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:149292800-149304800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:149292800-149321200	Weak transcription	Aorta	Aorta
42	chr6:149293000-149293600	Weak transcription	Spleen	Spleen
43	chr6:149293000-149294200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:149293000-149294200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:149293000-149296000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr6:149293200-149293800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:149293200-149293800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:149293200-149300400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:149293400-149293800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:149293400-149293800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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