Variant report

Variant	rs2842331
Chromosome Location	chr14:69010690-69010691
allele	A/C
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	EGR1	chr14:69010639-69011456	HCT-116	colon:	n/a	chr14:69010971-69010984 chr14:69010972-69010983 chr14:69010970-69010984 chr14:69010971-69010984 chr14:69010972-69010982 chr14:69010972-69010983 chr14:69010972-69010982 chr14:69010966-69010988
2	NFIC	chr14:69010408-69011447	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr14:69010283-69012485	MCF10A-Er-Src	breast:	n/a	n/a
4	PBX3	chr14:69010525-69011299	SK-N-SH	brain:	n/a	n/a
5	EGR1	chr14:69010686-69011302	HCT-116	colon:	n/a	chr14:69010971-69010984 chr14:69010972-69010983 chr14:69010970-69010984 chr14:69010971-69010984 chr14:69010972-69010982 chr14:69010972-69010983 chr14:69010972-69010982 chr14:69010966-69010988
6	POLR2A	chr14:69010249-69011449	U87	brain:	n/a	n/a
7	EP300	chr14:69010530-69011090	SK-N-SH_RA	brain:	n/a	n/a
8	RFX5	chr14:69010453-69011456	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr14:69010385-69011863	U87	brain:	n/a	n/a
10	POLR2A	chr14:69010334-69011863	U87	brain:	n/a	n/a
11	POLR2A	chr14:69010545-69011472	MCF10A-Er-Src	breast:	n/a	n/a
12	ESR1	chr14:69010529-69010873	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr14:69010524-69011121	SK-N-SH_RA	brain:	n/a	n/a
14	GATA3	chr14:69010440-69011348	SK-N-SH	brain:	n/a	chr14:69011224-69011232
15	ESR1	chr14:69010451-69010893	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69009163..69010827-chr14:69260601..69262528,2	MCF-7	breast:

Variant related genes	Relation type
RAD51B	TF binding region
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10134446	0.94[JPT][hapmap]
rs1023529	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs11158749	0.87[JPT][hapmap]
rs1476586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040782	0.85[AMR][1000 genomes]
rs2079211	0.92[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2107341	0.88[CEU][hapmap];0.90[AMR][1000 genomes]
rs2158358	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2189517	0.87[JPT][hapmap]
rs2244814	0.90[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs2247048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525522	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2525523	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525524	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842325	0.92[CHB][hapmap];0.85[AMR][1000 genomes]
rs2842329	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2842338	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7140266	0.94[JPT][hapmap]
rs757370	0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs916962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs929285	0.92[CHB][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9323513	0.86[JPT][hapmap]
rs9323514	0.86[JPT][hapmap]

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	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
4	nsv516239	chr14:69010690-69025870	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2842331	FAM71D	cis	parietal	SCAN
rs2842331	PLEKHG3	cis	cerebellum	SCAN
rs2842331	ATP6V1D	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69002400-69016600	Weak transcription	Gastric	stomach
2	chr14:69005000-69013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:69005000-69015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:69006000-69014600	Enhancers	NHDF-Ad	bronchial
5	chr14:69006200-69012000	Weak transcription	Lung	lung
6	chr14:69006400-69013200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:69006400-69013800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:69006800-69011200	Weak transcription	Placenta	Placenta
9	chr14:69006800-69011600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:69006800-69012800	Weak transcription	Esophagus	oesophagus
11	chr14:69006800-69013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:69006800-69014200	Weak transcription	Brain Substantia Nigra	brain
13	chr14:69006800-69014400	Weak transcription	Brain Hippocampus Middle	brain
14	chr14:69006800-69014600	Weak transcription	Brain Angular Gyrus	brain
15	chr14:69007000-69011000	Weak transcription	Left Ventricle	heart
16	chr14:69007000-69011400	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr14:69007200-69013400	Weak transcription	Right Ventricle	heart
18	chr14:69007400-69013600	Weak transcription	Fetal Heart	heart
19	chr14:69007800-69013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:69007800-69014000	Weak transcription	Brain Anterior Caudate	brain
21	chr14:69008000-69013800	Enhancers	HMEC	breast
22	chr14:69008000-69013800	Enhancers	HSMM	muscle
23	chr14:69008200-69013400	Weak transcription	Ovary	ovary
24	chr14:69008400-69010800	Weak transcription	Fetal Thymus	thymus
25	chr14:69008400-69010800	Weak transcription	Stomach Mucosa	stomach
26	chr14:69008400-69011000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr14:69008400-69011600	Weak transcription	Fetal Intestine Small	intestine
28	chr14:69008400-69011800	Weak transcription	Spleen	Spleen
29	chr14:69008400-69013600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr14:69008400-69013600	Weak transcription	Fetal Kidney	kidney
31	chr14:69008400-69013800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr14:69008400-69014200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:69009000-69012200	Enhancers	Osteobl	bone
34	chr14:69009000-69013400	Enhancers	NHEK	skin
35	chr14:69009000-69013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr14:69009000-69023600	Enhancers	Fetal Muscle Leg	muscle
37	chr14:69009200-69010800	Enhancers	Fetal Brain Male	brain
38	chr14:69009200-69012200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr14:69009200-69013400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr14:69009200-69016600	Enhancers	Colon Smooth Muscle	Colon
41	chr14:69009400-69013400	Enhancers	Rectal Smooth Muscle	rectum
42	chr14:69009400-69017600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:69009600-69014600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:69009600-69016000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr14:69009800-69010800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr14:69009800-69012400	Enhancers	Psoas Muscle	Psoas
47	chr14:69009800-69012400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr14:69009800-69013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr14:69010000-69011000	Weak transcription	Hela-S3	cervix
50	chr14:69010000-69011800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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