Variant report

Variant	rs1476610
Chromosome Location	chr14:71197755-71197756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71192214..71195072-chr14:71196372..71198780,2	K562	blood:
2	chr14:71196902..71199011-chr14:71204967..71206734,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10129307	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1034769	0.90[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs10873241	0.81[AFR][1000 genomes]
rs12589737	0.90[CEU][hapmap]
rs12879569	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2107666	0.90[CEU][hapmap]
rs2158526	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2158527	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2332455	0.84[AFR][1000 genomes]
rs2332458	0.90[CEU][hapmap]
rs3814872	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes]
rs4141095	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4899367	0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4899368	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4902852	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs6573978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573980	0.85[AFR][1000 genomes]
rs7140653	0.90[CEU][hapmap]
rs7152246	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7152516	0.90[CEU][hapmap];0.81[AFR][1000 genomes]
rs8006424	0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs8007131	0.85[AFR][1000 genomes]
rs8011047	0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8011507	0.84[AFR][1000 genomes]
rs8018294	0.85[AFR][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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1476610	MAP3K9	cis	cerebellum	SCAN
rs1476610	FAM71D	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71180800-71200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:71185400-71198800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr14:71185800-71198600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
5	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
7	chr14:71188600-71198600	Weak transcription	Liver	Liver
8	chr14:71188800-71198400	Strong transcription	HMEC	breast
9	chr14:71189800-71209400	Strong transcription	Fetal Brain Female	brain
10	chr14:71190000-71214400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
12	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr14:71191800-71198600	Weak transcription	HepG2	liver
14	chr14:71192200-71198000	Strong transcription	NHEK	skin
15	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
16	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr14:71193400-71211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:71193600-71199400	Strong transcription	A549	lung
19	chr14:71193600-71210200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:71193800-71209400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:71193800-71209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:71194000-71208400	Weak transcription	Brain Substantia Nigra	brain
23	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
24	chr14:71194200-71198200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:71194200-71209600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr14:71194400-71201800	Weak transcription	Right Atrium	heart
27	chr14:71194400-71210400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:71194400-71213400	Weak transcription	Psoas Muscle	Psoas
29	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
30	chr14:71194600-71198000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:71194600-71198600	Weak transcription	Right Ventricle	heart
32	chr14:71194600-71198600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr14:71194800-71199400	Weak transcription	Brain Hippocampus Middle	brain
36	chr14:71195000-71198800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr14:71195200-71198400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:71195400-71197800	Strong transcription	Esophagus	oesophagus
39	chr14:71195400-71198400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr14:71195400-71200800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:71195400-71200800	Strong transcription	Primary B cells from cord blood	blood
42	chr14:71195400-71201600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:71195600-71200200	Strong transcription	Pancreas	Pancrea
44	chr14:71195600-71202200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr14:71195600-71209400	Strong transcription	Placenta	Placenta
46	chr14:71195600-71209600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr14:71195600-71210000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr14:71196000-71198200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:71196000-71199000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr14:71196000-71199200	Weak transcription	Ovary	ovary

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