Variant report

Variant	rs2153631
Chromosome Location	chr1:247462048-247462049
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	chr1:247462027..247464114-chr1:247493562..247495364,2	K562	blood:
2	chr1:247461556..247465350-chr1:247467126..247471967,7	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10754542	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10754544	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10924983	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10924985	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11578583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1192830	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1192832	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12035515	0.86[ASN][1000 genomes]
rs1204493	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341173	0.81[ASN][1000 genomes]
rs1616299	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771929	0.83[ASN][1000 genomes]
rs1771943	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1771948	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778544	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778546	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778549	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799540	0.83[ASN][1000 genomes]
rs3850824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925532	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925533	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925534	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925615	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925621	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56037169	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56399534	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674425	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74163745	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7418221	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7528202	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540329	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552292	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs875883	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426180	0.85[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426181	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426182	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426233	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9725334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]

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	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	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
4	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
5	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2153631	OR2T11	cis	parietal	SCAN
rs2153631	ZNF496	cis	Nerve Tibial	GTEx
rs2153631	EDIL3	trans	lymphoblastoid	RTeQTL
rs2153631	ZNF496	cis	lung	GTEx
rs2153631	ZNF496	cis	parietal	SCAN
rs2153631	ZNF496	cis	Thyroid	GTEx
rs2153631	MAP1LC3C	cis	parietal	SCAN
rs2153631	ZNF496	cis	cerebellum	SCAN
rs2153631	ZNF496	cis	Esophagus Muscularis	GTEx
rs2153631	ZNF496	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
2	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
4	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
5	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
11	chr1:247456200-247462200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
13	chr1:247456800-247462200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:247456800-247462400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:247457000-247465000	Weak transcription	Hela-S3	cervix
16	chr1:247457800-247463200	Weak transcription	Placenta	Placenta
17	chr1:247457800-247466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:247458000-247466800	Weak transcription	HSMMtube	muscle
19	chr1:247458200-247462200	Weak transcription	HSMM	muscle
20	chr1:247458200-247462400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:247458200-247463000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:247459000-247462200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:247459000-247462200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:247459000-247462400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:247459000-247462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:247459000-247463600	Weak transcription	NH-A	brain
27	chr1:247459000-247463600	Weak transcription	NHLF	lung
28	chr1:247459200-247463600	Weak transcription	Osteobl	bone
29	chr1:247459400-247462600	Weak transcription	Fetal Intestine Small	intestine
30	chr1:247459400-247463200	Weak transcription	Left Ventricle	heart
31	chr1:247459600-247463600	Weak transcription	Fetal Lung	lung
32	chr1:247459800-247462400	Weak transcription	Spleen	Spleen
33	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:247460200-247462400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:247460200-247462400	Weak transcription	NHEK	skin
36	chr1:247460400-247462200	Weak transcription	Fetal Intestine Large	intestine
37	chr1:247460400-247463000	Weak transcription	GM12878-XiMat	blood
38	chr1:247460400-247464000	Strong transcription	Fetal Stomach	stomach
39	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
40	chr1:247460600-247462200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:247460600-247462400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:247460600-247462400	Weak transcription	Dnd41	blood
43	chr1:247460600-247463600	Strong transcription	A549	lung
44	chr1:247460800-247462400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:247460800-247462400	Weak transcription	Liver	Liver
46	chr1:247460800-247462600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:247460800-247462800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:247460800-247463000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:247460800-247463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:247460800-247463000	Weak transcription	HepG2	liver

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