Variant report

Variant	rs4925536
Chromosome Location	chr1:247508452-247508453
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247494726..247499261-chr1:247506139..247509123,5	MCF-7	breast:
2	chr1:247497043..247499378-chr1:247507440..247508988,2	MCF-7	breast:
3	chr1:247505878..247508522-chr1:247514290..247518138,3	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11585647	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55863520	0.89[EUR][1000 genomes]
rs60631274	0.80[EUR][1000 genomes]
rs60859377	0.85[EUR][1000 genomes]
rs73134241	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4925536	FAM36A	cis	parietal	SCAN
rs4925536	OR2B11	cis	parietal	SCAN
rs4925536	PPPDE1	cis	cerebellum	SCAN
rs4925536	VN1R5	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247496400-247511000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:247496600-247511000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:247496800-247510200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:247497000-247511200	Weak transcription	Esophagus	oesophagus
5	chr1:247497200-247509800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:247497200-247516000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:247497400-247511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:247497400-247511400	Weak transcription	Primary T cells from cord blood	blood
9	chr1:247499600-247511000	Weak transcription	Adipose Nuclei	Adipose
10	chr1:247499600-247511200	Weak transcription	Brain Germinal Matrix	brain
11	chr1:247499800-247510800	Weak transcription	Right Atrium	heart
12	chr1:247500800-247511800	Weak transcription	Fetal Kidney	kidney
13	chr1:247501000-247510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:247501400-247511200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:247501600-247537000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:247502000-247508600	Weak transcription	Fetal Brain Male	brain
17	chr1:247503400-247511000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:247503600-247510400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:247503600-247510600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:247503600-247511000	Weak transcription	Ovary	ovary
21	chr1:247503600-247511000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:247503600-247511200	Weak transcription	Placenta	Placenta
23	chr1:247503600-247511200	Weak transcription	Left Ventricle	heart
24	chr1:247503600-247511200	Weak transcription	Lung	lung
25	chr1:247503600-247511200	Weak transcription	Right Ventricle	heart
26	chr1:247503600-247511400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:247503600-247511400	Weak transcription	Spleen	Spleen
28	chr1:247503600-247516400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:247503800-247511000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:247504000-247511200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:247504200-247508600	Weak transcription	HepG2	liver
32	chr1:247504200-247510600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:247504800-247509200	Weak transcription	Fetal Brain Female	brain
34	chr1:247504800-247511200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:247504800-247520600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:247505000-247511200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:247505200-247511000	Weak transcription	Fetal Thymus	thymus
38	chr1:247505200-247511200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:247505400-247509400	Weak transcription	Fetal Stomach	stomach
40	chr1:247505400-247510400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:247505400-247511000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:247505400-247511000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:247505400-247511000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:247505400-247511000	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:247505400-247511000	Weak transcription	Thymus	Thymus
46	chr1:247505400-247511200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:247505400-247511200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:247505400-247511200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:247505600-247511000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:247506400-247510000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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