Variant report

Variant	rs2842329
Chromosome Location	chr14:69017595-69017596
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69015136..69018224-chr14:69257957..69260697,4	MCF-7	breast:
2	chr14:68752714..68755212-chr14:69016133..69017803,2	MCF-7	breast:
3	chr14:68943428..68945388-chr14:69016683..69019444,2	MCF-7	breast:
4	chr14:68932051..68934015-chr14:69017184..69019251,2	MCF-7	breast:
5	chr14:69006886..69009005-chr14:69017187..69019247,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10134446	0.88[JPT][hapmap]
rs1023529	0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11158749	0.81[JPT][hapmap]
rs1476586	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1859302	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2040782	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2079211	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2158358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189517	0.81[JPT][hapmap]
rs2244814	0.89[CHB][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2247048	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2525521	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2525522	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2525523	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2525524	0.84[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2525525	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2525526	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2525527	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2842325	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2842331	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	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7140266	0.88[JPT][hapmap]
rs757370	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs916962	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs929285	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[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	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
rs2842329	PLEKHG3	cis	cerebellum	SCAN
rs2842329	ATP6V1D	cis	cerebellum	SCAN
rs2842329	C14orf50	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69009000-69023600	Enhancers	Fetal Muscle Leg	muscle
2	chr14:69009400-69017600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:69010400-69018600	Enhancers	Fetal Stomach	stomach
4	chr14:69010800-69017800	Enhancers	Stomach Mucosa	stomach
5	chr14:69011400-69018000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr14:69012600-69018400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr14:69012800-69019400	Enhancers	Left Ventricle	heart
8	chr14:69012800-69022000	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr14:69013000-69019200	Enhancers	Right Atrium	heart
10	chr14:69013400-69018600	Enhancers	Ovary	ovary
11	chr14:69013400-69022600	Enhancers	HUVEC	blood vessel
12	chr14:69013600-69019000	Enhancers	Fetal Heart	heart
13	chr14:69013600-69019800	Enhancers	Fetal Kidney	kidney
14	chr14:69013600-69021200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr14:69013600-69022600	Enhancers	Adipose Nuclei	Adipose
16	chr14:69013800-69018200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr14:69013800-69018200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:69014000-69018200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr14:69014000-69018400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr14:69014000-69018600	Enhancers	Fetal Brain Male	brain
21	chr14:69014200-69018200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:69014200-69018200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:69014200-69018600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:69014200-69021000	Weak transcription	Small Intestine	intestine
25	chr14:69014400-69017800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:69014400-69018800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr14:69014400-69019400	Enhancers	Placenta	Placenta
28	chr14:69014400-69022600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:69014400-69022800	Enhancers	Rectal Smooth Muscle	rectum
30	chr14:69014600-69017800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr14:69015000-69017800	Enhancers	HSMM	muscle
32	chr14:69015400-69020400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:69015600-69017600	Enhancers	Fetal Intestine Small	intestine
34	chr14:69015600-69017800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:69015600-69018400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr14:69015600-69018800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr14:69015600-69020400	Enhancers	HMEC	breast
38	chr14:69015600-69021800	Enhancers	HSMMtube	muscle
39	chr14:69015800-69017800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr14:69015800-69017800	Weak transcription	Esophagus	oesophagus
41	chr14:69015800-69018000	Enhancers	NHLF	lung
42	chr14:69015800-69020400	Enhancers	Stomach Smooth Muscle	stomach
43	chr14:69015800-69022000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr14:69015800-69022600	Enhancers	NHDF-Ad	bronchial
45	chr14:69015800-69022800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:69015800-69023000	Weak transcription	Aorta	Aorta
47	chr14:69016000-69017600	Weak transcription	Fetal Brain Female	brain
48	chr14:69016000-69017800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr14:69016000-69017800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr14:69016000-69017800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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