Variant report

Variant	rs17105812
Chromosome Location	chr14:69008327-69008328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr14:69007808-69008444	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr14:69007843-69008422	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr14:69007775-69008375	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:69001801..69004663-chr14:69006865..69008433,2	MCF-7	breast:
2	chr14:69006886..69009005-chr14:69017187..69019247,2	MCF-7	breast:
3	chr14:69007812..69009771-chr14:69024457..69026624,2	MCF-7	breast:

Variant related genes	Relation type
RAD51B	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10130177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134240	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137367	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147979	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148391	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483810	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10483811	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483814	1.00[CHB][hapmap]
rs11849344	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105826	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs17105828	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829180	1.00[CHB][hapmap]
rs17829192	1.00[CHB][hapmap]
rs28377700	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842339	1.00[CHB][hapmap]
rs28454359	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492919	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28558877	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28671277	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59404246	1.00[ASN][1000 genomes]
rs6573841	0.83[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs72727502	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729521	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016149	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs8017678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323515	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1048064	chr14:68991041-69012766	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17105812	FAM71D	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69002400-69016600	Weak transcription	Gastric	stomach
2	chr14:69003000-69009000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr14:69003200-69009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:69003600-69009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:69003600-69009000	Weak transcription	NHEK	skin
6	chr14:69004400-69008600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:69004600-69008400	Enhancers	Brain Germinal Matrix	brain
8	chr14:69004600-69009800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr14:69004600-69010600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:69004800-69008600	Enhancers	Fetal Muscle Leg	muscle
11	chr14:69005000-69008400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr14:69005000-69008800	Enhancers	Colon Smooth Muscle	Colon
13	chr14:69005000-69008800	Enhancers	Fetal Stomach	stomach
14	chr14:69005000-69010400	Weak transcription	Pancreas	Pancrea
15	chr14:69005000-69013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:69005000-69015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:69005400-69008400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr14:69006000-69014600	Enhancers	NHDF-Ad	bronchial
19	chr14:69006200-69010400	Weak transcription	Aorta	Aorta
20	chr14:69006200-69012000	Weak transcription	Lung	lung
21	chr14:69006400-69013200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr14:69006400-69013800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:69006600-69008400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:69006600-69008400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr14:69006800-69009200	Weak transcription	Fetal Brain Male	brain
26	chr14:69006800-69010200	Weak transcription	Fetal Lung	lung
27	chr14:69006800-69010400	Weak transcription	HSMMtube	muscle
28	chr14:69006800-69011200	Weak transcription	Placenta	Placenta
29	chr14:69006800-69011600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr14:69006800-69012800	Weak transcription	Esophagus	oesophagus
31	chr14:69006800-69013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:69006800-69014200	Weak transcription	Brain Substantia Nigra	brain
33	chr14:69006800-69014400	Weak transcription	Brain Hippocampus Middle	brain
34	chr14:69006800-69014600	Weak transcription	Brain Angular Gyrus	brain
35	chr14:69007000-69011000	Weak transcription	Left Ventricle	heart
36	chr14:69007000-69011400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr14:69007200-69013400	Weak transcription	Right Ventricle	heart
38	chr14:69007400-69008400	Enhancers	Fetal Kidney	kidney
39	chr14:69007400-69008400	Enhancers	Fetal Thymus	thymus
40	chr14:69007400-69008400	Enhancers	Stomach Smooth Muscle	stomach
41	chr14:69007400-69013600	Weak transcription	Fetal Heart	heart
42	chr14:69007800-69008400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr14:69007800-69008400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr14:69007800-69008400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr14:69007800-69008400	Enhancers	Psoas Muscle	Psoas
46	chr14:69007800-69008400	Enhancers	Stomach Mucosa	stomach
47	chr14:69007800-69008600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr14:69007800-69010000	Enhancers	Hela-S3	cervix
49	chr14:69007800-69013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr14:69007800-69014000	Weak transcription	Brain Anterior Caudate	brain

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