Variant report

Variant	rs16847544
Chromosome Location	chr1:165570840-165570841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:165565977..165568416-chr1:165569546..165571899,2	K562	blood:
2	chr1:165569088..165572600-chr1:165598003..165601699,3	K562	blood:
3	chr1:165570598..165571161-chr1:165885123..165885647,2	K562	blood:
4	chr1:165570586..165571293-chr1:165883467..165884080,3	MCF-7	breast:
5	chr1:165569692..165572245-chr1:165736970..165738543,2	K562	blood:
6	chr1:165570516..165571146-chr1:165883471..165884311,2	MCF-7	breast:
7	chr1:165570621..165571411-chr1:165655068..165656040,3	MCF-7	breast:
8	chr1:165568647..165571505-chr1:165795399..165798198,2	MCF-7	breast:
9	chr1:165569014..165571063-chr1:165883495..165885234,2	K562	blood:
10	chr1:165570583..165571677-chr1:165883154..165884275,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000236206	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10800127	1.00[CHB][hapmap]
rs11506	1.00[CHB][hapmap]
rs11799886	1.00[JPT][hapmap]
rs11799903	1.00[JPT][hapmap]
rs11800476	1.00[CHB][hapmap]
rs11801044	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11801981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802672	1.00[ASN][1000 genomes]
rs11803276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16847487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57256442	0.89[ASN][1000 genomes]
rs58045866	1.00[ASN][1000 genomes]
rs59033716	1.00[ASN][1000 genomes]
rs61557603	0.89[ASN][1000 genomes]
rs61804068	0.89[ASN][1000 genomes]
rs61804069	0.89[ASN][1000 genomes]
rs6682771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686643	1.00[JPT][hapmap]
rs6693448	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs6695758	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]
rs72696026	1.00[ASN][1000 genomes]
rs72696027	1.00[ASN][1000 genomes]
rs72696028	1.00[ASN][1000 genomes]
rs72696029	1.00[ASN][1000 genomes]
rs7516587	1.00[JPT][hapmap]
rs7550682	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554034	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9333378	1.00[JPT][hapmap]
rs9333464	1.00[JPT][hapmap]
rs9333471	1.00[JPT][hapmap]
rs959617	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429902	chr1:165531342-165574342	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16847544	ILDR2	cis	parietal	SCAN
rs16847544	ITLN1	cis	parietal	SCAN
rs16847544	MPZ	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165568000-165572800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:165568000-165574800	Weak transcription	Right Atrium	heart
3	chr1:165568200-165571000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:165568200-165571000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:165568200-165571000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:165568200-165571000	Enhancers	HepG2	liver
7	chr1:165568200-165579600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:165568600-165571000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:165568600-165571000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:165568600-165571000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:165569000-165571000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:165569000-165571200	Weak transcription	Osteobl	bone
13	chr1:165569600-165571000	Enhancers	Liver	Liver
14	chr1:165569800-165571200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr1:165569800-165571400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:165569800-165571400	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:165570400-165571000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:165570600-165571000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:165570600-165571000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:165570600-165571000	Enhancers	Brain Hippocampus Middle	brain
21	chr1:165570600-165571400	Enhancers	Stomach Mucosa	stomach
22	chr1:165570800-165571000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:165570800-165571000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:165570800-165571000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:165570800-165571000	Enhancers	Adipose Nuclei	Adipose
26	chr1:165570800-165571000	Enhancers	Fetal Heart	heart
27	chr1:165570800-165571000	Enhancers	Hela-S3	cervix
28	chr1:165570800-165571200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:165570800-165571200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:165570800-165571200	Enhancers	Brain Anterior Caudate	brain
31	chr1:165570800-165571200	Enhancers	Brain Substantia Nigra	brain
32	chr1:165570800-165571200	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr1:165570800-165571200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:165570800-165571200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr1:165570800-165571200	Enhancers	GM12878-XiMat	blood
36	chr1:165570800-165571400	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:165570800-165571400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:165570800-165571400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:165570800-165571400	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:165570800-165571400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:165570800-165571400	Enhancers	Colon Smooth Muscle	Colon
42	chr1:165570800-165571400	Enhancers	Fetal Intestine Small	intestine
43	chr1:165570800-165571400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr1:165570800-165571400	Enhancers	A549	lung
45	chr1:165570800-165571400	Flanking Active TSS	K562	blood

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