Variant report

Variant	rs2064929
Chromosome Location	chr14:68025260-68025261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:67999813..68002662-chr14:68023005..68026925,3	MCF-7	breast:
2	chr14:67999778..68002344-chr14:68024598..68027003,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198133	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11158681	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158682	0.91[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11158683	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11158684	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12433356	0.87[CHB][hapmap]
rs12434659	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12589605	0.87[CHB][hapmap]
rs17836795	0.87[CHB][hapmap]
rs4144498	0.84[MEX][hapmap]
rs4902478	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4902479	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4902482	0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4902483	0.92[CEU][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes]
rs4902484	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902486	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7147529	0.87[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7154636	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7155887	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs731681	0.84[MEX][hapmap]
rs753683	0.80[CEU][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	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2064929	FUT8	cis	parietal	SCAN
rs2064929	C14orf181	cis	cerebellum	SCAN
rs2064929	PLEKHH1	cis	cerebellum	SCAN
rs2064929	ADAM20	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
2	chr14:68001400-68028400	Weak transcription	Brain Germinal Matrix	brain
3	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
4	chr14:68003200-68039800	Weak transcription	Fetal Kidney	kidney
5	chr14:68005800-68042400	Weak transcription	NHEK	skin
6	chr14:68008800-68052200	Weak transcription	Left Ventricle	heart
7	chr14:68009000-68044800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr14:68009000-68050400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr14:68009200-68040400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr14:68009200-68045200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr14:68010200-68036400	Weak transcription	Small Intestine	intestine
12	chr14:68011800-68045000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr14:68011800-68054600	Weak transcription	Hela-S3	cervix
14	chr14:68012000-68029200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:68012000-68033000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:68012000-68045000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:68012400-68025600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr14:68012400-68026200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:68012400-68028200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr14:68012400-68028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr14:68012800-68026200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr14:68013400-68052600	Weak transcription	Aorta	Aorta
23	chr14:68014400-68036200	Weak transcription	Colonic Mucosa	Colon
24	chr14:68016000-68033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:68016800-68025400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr14:68016800-68028800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr14:68018600-68042400	Weak transcription	Right Ventricle	heart
28	chr14:68020200-68027400	Genic enhancers	Brain Substantia Nigra	brain
29	chr14:68020400-68025600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr14:68020800-68033600	Weak transcription	Stomach Mucosa	stomach
31	chr14:68021000-68030200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr14:68021400-68032200	Strong transcription	Brain Anterior Caudate	brain
33	chr14:68022000-68029800	Strong transcription	Fetal Stomach	stomach
34	chr14:68022200-68025400	Genic enhancers	Brain Hippocampus Middle	brain
35	chr14:68022600-68026600	Enhancers	Placenta	Placenta
36	chr14:68022800-68053000	Weak transcription	Lung	lung
37	chr14:68023400-68026600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr14:68023400-68026600	Enhancers	HMEC	breast
39	chr14:68023600-68025400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr14:68023600-68025800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr14:68023600-68026400	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr14:68023600-68026600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:68023800-68025800	Strong transcription	Pancreas	Pancrea
44	chr14:68023800-68026400	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr14:68024000-68025600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:68024000-68030200	Strong transcription	Fetal Brain Female	brain
47	chr14:68024200-68038000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:68024400-68033000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:68024600-68026000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr14:68024600-68026800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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