Variant report

Variant	rs6429339
Chromosome Location	chr1:242375779-242375780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2164417	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs316854	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316856	0.85[EUR][1000 genomes]
rs316857	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs316863	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs316899	0.81[EUR][1000 genomes]
rs377453	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs383039	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs392351	0.86[EUR][1000 genomes]
rs397507	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs426314	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs427565	0.85[EUR][1000 genomes]
rs429753	0.86[EUR][1000 genomes]
rs433675	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs434200	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv468672	chr1:242201247-242555949	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv470788	chr1:242201247-242555949	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv549462	chr1:242201247-242555949	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv528016	chr1:242223399-242451350	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv549463	chr1:242265419-242856854	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv998804	chr1:242281003-242491362	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv430391	chr1:242307104-243280885	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv817488	chr1:242330066-243121127	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv868888	chr1:242330066-243191101	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1003844	chr1:242363698-242904755	Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6429339	PLD5	cis	cerebellum	SCAN
rs6429339	CHML	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242353400-242380400	Weak transcription	Aorta	Aorta
2	chr1:242364000-242379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:242369600-242378600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:242371000-242386600	Weak transcription	HMEC	breast
5	chr1:242371400-242376400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:242371600-242377600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:242372600-242377800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:242372800-242377000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:242372800-242377000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:242373600-242376000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:242373600-242376400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr1:242374000-242375800	Enhancers	Fetal Intestine Small	intestine
13	chr1:242374000-242376000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:242374000-242376000	Enhancers	Pancreas	Pancrea
15	chr1:242374000-242377000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:242374000-242377200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:242374000-242377200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:242374200-242376000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:242374200-242377400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:242374200-242377600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:242374800-242375800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:242374800-242376000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:242374800-242376000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:242374800-242376000	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:242375000-242375800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:242375000-242376000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:242375400-242376000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:242375400-242376000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:242375400-242376400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr1:242375600-242376000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:242375600-242378000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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