Variant report

Variant	rs6573841
Chromosome Location	chr14:69037521-69037522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:69034895..69037596-chr14:69073887..69076844,4	MCF-7	breast:
2	chr14:68925458..68926396-chr14:69036429..69037582,24	MCF-7	breast:
3	chr14:68925011..68926542-chr14:69036351..69037638,115	MCF-7	breast:
4	chr14:69008510..69012308-chr14:69035243..69038213,3	MCF-7	breast:
5	chr14:68772189..68774802-chr14:69035242..69038239,3	MCF-7	breast:
6	chr14:69027264..69032673-chr14:69034374..69038789,10	MCF-7	breast:
7	chr14:69036779..69038286-chr14:69038694..69040198,2	MCF-7	breast:
8	chr14:69037050..69041400-chr14:69041759..69045325,4	MCF-7	breast:
9	chr14:68925379..68928137-chr14:69035379..69037742,2	MCF-7	breast:
10	chr14:69028863..69039900-chr14:69256962..69265663,39	MCF-7	breast:
11	chr14:69035875..69039894-chr14:69250533..69252732,3	MCF-7	breast:
12	chr14:69034578..69039415-chr14:69094170..69096793,5	MCF-7	breast:
13	chr14:68746918..68749020-chr14:69036355..69038421,2	MCF-7	breast:
14	chr14:69036750..69039509-chr14:69055628..69057571,2	MCF-7	breast:
15	chr14:69027748..69038857-chr14:69257974..69264472,24	MCF-7	breast:
16	chr14:69037043..69039737-chr5:178416240..178417937,2	MCF-7	breast:
17	chr14:69036141..69039001-chr14:69250831..69253472,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259038	Chromatin interaction
ENSG00000182185	Chromatin interaction
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10130177	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs10134240	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10137367	0.89[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10147979	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs10148391	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10483811	0.89[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11849344	0.89[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs17105810	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs17105812	0.83[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs17105822	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17105828	0.83[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs17105829	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs2428616	1.00[JPT][hapmap]
rs2525502	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2525504	0.81[GIH][hapmap]
rs2525515	1.00[JPT][hapmap]
rs2525517	1.00[JPT][hapmap]
rs2525518	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2525529	1.00[JPT][hapmap]
rs28377700	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2842332	1.00[JPT][hapmap]
rs2842335	1.00[JPT][hapmap]
rs2842336	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2842337	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2842343	0.83[CHD][hapmap]
rs2842344	0.83[CHD][hapmap]
rs28454359	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28492919	0.94[EUR][1000 genomes]
rs28558877	0.91[EUR][1000 genomes]
rs28671277	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7153476	0.89[CHD][hapmap]
rs72727502	0.87[EUR][1000 genomes]
rs72729521	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs727392	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs8007194	0.89[CHD][hapmap]
rs8016149	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs8017678	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs9323515	0.89[CEU][hapmap];0.89[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	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	esv1795754	chr14:69017623-69079110	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1832715	chr14:69017623-69079110	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6573841	FAM71D	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69030800-69041600	Weak transcription	NHLF	lung
2	chr14:69031200-69041800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:69032400-69041400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr14:69032800-69040800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:69033000-69039600	Weak transcription	Primary T cells from cord blood	blood
6	chr14:69033200-69041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:69033400-69039400	Weak transcription	Spleen	Spleen
8	chr14:69033600-69041600	Weak transcription	Hela-S3	cervix
9	chr14:69034400-69037800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr14:69034400-69038000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:69035000-69039400	Enhancers	Pancreas	Pancrea
12	chr14:69035200-69038000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:69035400-69037800	Enhancers	HUVEC	blood vessel
14	chr14:69035400-69039200	Enhancers	Liver	Liver
15	chr14:69035600-69037600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr14:69035600-69037600	Enhancers	Fetal Thymus	thymus
17	chr14:69035600-69037800	Enhancers	Lung	lung
18	chr14:69036400-69041000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr14:69036600-69039800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:69036800-69038000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:69036800-69041400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr14:69036800-69052000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr14:69037000-69039600	Enhancers	HepG2	liver
24	chr14:69037000-69039800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr14:69037000-69041600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr14:69037000-69041600	Weak transcription	Psoas Muscle	Psoas
27	chr14:69037000-69041800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:69037000-69042000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr14:69037000-69052600	Weak transcription	Colonic Mucosa	Colon
30	chr14:69037200-69039000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:69037200-69040400	Weak transcription	Brain Hippocampus Middle	brain
32	chr14:69037200-69041600	Weak transcription	Ovary	ovary
33	chr14:69037200-69041600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:69037400-69037800	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:69037400-69038600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr14:69037400-69040600	Weak transcription	Adipose Nuclei	Adipose
37	chr14:69037400-69041000	Weak transcription	Placenta	Placenta
38	chr14:69037400-69041200	Weak transcription	Brain Anterior Caudate	brain
39	chr14:69037400-69041400	Weak transcription	Fetal Lung	lung
40	chr14:69037400-69041600	Weak transcription	Fetal Heart	heart
41	chr14:69037400-69041600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:69037400-69042800	Weak transcription	Gastric	stomach
43	chr14:69037400-69042800	Weak transcription	Right Ventricle	heart
44	chr14:69037400-69042800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr14:69037400-69054000	Weak transcription	Fetal Kidney	kidney

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