Variant report

Variant	rs16847690
Chromosome Location	chr1:227544513-227544514
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	chr1:227500332..227503244-chr1:227542452..227546426,3	K562	blood:
2	chr1:227538699..227541484-chr1:227541523..227544732,3	K562	blood:
3	chr1:227530004..227531829-chr1:227543637..227545711,2	K562	blood:
4	chr1:227504395..227506976-chr1:227543254..227545122,2	MCF-7	breast:
5	chr1:227544242..227546740-chr1:227566888..227569637,2	K562	blood:
6	chr1:227530329..227533212-chr1:227543637..227546131,2	K562	blood:
7	chr1:227542971..227547040-chr1:227548442..227550941,4	K562	blood:
8	chr1:227503674..227505956-chr1:227543309..227545272,2	MCF-7	breast:
9	chr1:227538792..227542003-chr1:227542964..227545271,3	K562	blood:
10	chr1:227502375..227508330-chr1:227544221..227551404,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10458380	0.81[ASN][1000 genomes]
rs10753434	0.86[ASN][1000 genomes]
rs10799412	0.86[ASN][1000 genomes]
rs10916123	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916124	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916127	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916128	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916129	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10916133	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap]
rs12022275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023427	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028523	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035190	0.82[ASW][hapmap]
rs12047964	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062358	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12081061	0.81[CEU][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085773	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16847682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654860	0.90[ASN][1000 genomes]
rs4075196	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4075861	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233226	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4233227	0.82[CHB][hapmap]
rs4294380	0.80[CHB][hapmap]
rs4531260	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653497	1.00[ASN][1000 genomes]
rs4653498	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs4653826	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4653828	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653831	0.92[ASN][1000 genomes]
rs59718661	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61833060	1.00[ASN][1000 genomes]
rs6690898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67343057	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72632826	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72759365	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519870	0.99[ASN][1000 genomes]
rs7540726	0.82[ASN][1000 genomes]
rs7540833	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553358	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555764	0.87[ASN][1000 genomes]
rs7556096	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16847690	PGAM2	trans	parietal	SCAN
rs16847690	ARF1	cis	cerebellum	SCAN
rs16847690	CCDC67	trans	parietal	SCAN
rs16847690	CNIH4	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227539200-227545000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227539400-227545000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:227539600-227544600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:227539600-227544800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:227542600-227547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:227542800-227545800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:227543400-227544600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227543400-227544600	Enhancers	K562	blood
9	chr1:227543400-227545800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:227543600-227544600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:227543600-227545000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:227543600-227545800	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:227544000-227546200	Enhancers	Fetal Intestine Large	intestine
14	chr1:227544200-227544600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:227544200-227544600	Enhancers	NHDF-Ad	bronchial
16	chr1:227544200-227544800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:227544200-227544800	Enhancers	HMEC	breast
18	chr1:227544200-227545000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:227544200-227545000	Enhancers	Spleen	Spleen
20	chr1:227544200-227545000	Enhancers	HSMM	muscle
21	chr1:227544200-227545000	Enhancers	Osteobl	bone
22	chr1:227544200-227545200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:227544200-227545200	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr1:227544200-227545800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:227544200-227545800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:227544200-227545800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:227544200-227545800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:227544200-227545800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:227544200-227545800	Enhancers	Adipose Nuclei	Adipose
30	chr1:227544200-227545800	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:227544200-227545800	Enhancers	Fetal Muscle Leg	muscle
32	chr1:227544200-227545800	Enhancers	Placenta	Placenta
33	chr1:227544200-227545800	Enhancers	Left Ventricle	heart
34	chr1:227544200-227545800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:227544200-227545800	Flanking Active TSS	A549	lung
36	chr1:227544200-227545800	Flanking Active TSS	Hela-S3	cervix
37	chr1:227544200-227545800	Flanking Active TSS	HUVEC	blood vessel
38	chr1:227544200-227545800	Enhancers	NH-A	brain
39	chr1:227544200-227546000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:227544200-227546000	Enhancers	Fetal Intestine Small	intestine
41	chr1:227544200-227546000	Enhancers	Stomach Mucosa	stomach
42	chr1:227544200-227546000	Enhancers	NHLF	lung
43	chr1:227544200-227546200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:227544200-227546400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:227544200-227546600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:227544200-227547600	Enhancers	Lung	lung
47	chr1:227544400-227544600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr1:227544400-227544600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr1:227544400-227544600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:227544400-227544600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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