Variant report

Variant	rs1034769
Chromosome Location	chr14:71254698-71254699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71254174..71260054-chr14:71263244..71266960,6	MCF-7	breast:
2	chr14:71253814..71258557-chr14:71260999..71264904,5	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10129307	0.81[CEU][hapmap]
rs10873241	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873242	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12589737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12879569	0.81[GIH][hapmap]
rs1476609	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs1476610	0.90[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs2023955	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs2107665	0.91[CHB][hapmap]
rs2107666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332455	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2332458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141095	0.90[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs4899368	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4899369	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902844	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4902852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902863	0.91[CHB][hapmap]
rs6573978	0.90[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs6573980	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7152516	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7155910	0.91[CHB][hapmap]
rs8007131	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8011047	0.86[GIH][hapmap]
rs8011507	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8018294	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1034769	FAM71D	cis	cerebellum	SCAN
rs1034769	DPF3	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
2	chr14:71222200-71258200	Weak transcription	HepG2	liver
3	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
4	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
5	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:71224000-71258000	Weak transcription	Dnd41	blood
7	chr14:71227800-71257800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr14:71228000-71258000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:71228000-71258000	Weak transcription	A549	lung
10	chr14:71228200-71258000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:71238600-71266600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:71239000-71258000	Weak transcription	Fetal Intestine Small	intestine
13	chr14:71239000-71269600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:71239200-71258200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:71239400-71258200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:71239800-71258400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:71240000-71258000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:71240200-71257800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:71240600-71255600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:71240600-71258000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr14:71242400-71258200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:71242400-71266600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr14:71242600-71266200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr14:71244200-71255800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:71245800-71255200	Weak transcription	Psoas Muscle	Psoas
26	chr14:71246200-71258000	Weak transcription	Brain Germinal Matrix	brain
27	chr14:71246800-71255800	Weak transcription	Spleen	Spleen
28	chr14:71246800-71266800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:71247000-71258200	Weak transcription	Liver	Liver
30	chr14:71247400-71266600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr14:71247600-71256600	Weak transcription	Placenta	Placenta
32	chr14:71247800-71274600	Weak transcription	Stomach Mucosa	stomach
33	chr14:71248200-71258000	Weak transcription	Gastric	stomach
34	chr14:71248200-71258000	Weak transcription	Pancreas	Pancrea
35	chr14:71248200-71271200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:71248800-71257400	Weak transcription	Primary B cells from cord blood	blood
37	chr14:71249000-71266400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr14:71249400-71266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr14:71249400-71266600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr14:71249400-71266600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr14:71249400-71274400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr14:71249400-71274400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr14:71249400-71274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr14:71249600-71258600	Weak transcription	GM12878-XiMat	blood
45	chr14:71249600-71274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr14:71249800-71255000	Weak transcription	HSMM	muscle
47	chr14:71249800-71255200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr14:71249800-71256200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr14:71249800-71274600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr14:71250400-71266600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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