Variant report

Variant	rs55814152
Chromosome Location	chr1:212460687-212460688
allele	C/G
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212206622..212210088-chr1:212456790..212460936,6	K562	blood:
2	chr1:212459558..212461570-chr1:212482463..212485190,2	K562	blood:
3	chr1:212459145..212461703-chr1:212522964..212525110,2	K562	blood:
4	chr1:212247974..212251489-chr1:212456327..212461743,5	MCF-7	breast:
5	chr1:212413271..212416807-chr1:212458908..212461742,4	K562	blood:
6	chr1:210546264..210548680-chr1:212458394..212460879,2	K562	blood:
7	chr1:212270755..212277124-chr1:212457942..212461824,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143493	Chromatin interaction
ENSG00000264358	Chromatin interaction
ENSG00000225338	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000252879	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10863960	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863961	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863963	0.87[EUR][1000 genomes]
rs11119899	0.92[ASN][1000 genomes]
rs11119919	0.86[EUR][1000 genomes]
rs11119920	0.87[EUR][1000 genomes]
rs11119924	0.85[EUR][1000 genomes]
rs11576437	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11576769	0.86[EUR][1000 genomes]
rs11580285	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11584189	0.84[EUR][1000 genomes]
rs11585215	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587555	0.86[EUR][1000 genomes]
rs11588867	0.83[EUR][1000 genomes]
rs11589817	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11590242	0.85[EUR][1000 genomes]
rs11590672	0.81[EUR][1000 genomes]
rs12064553	0.85[EUR][1000 genomes]
rs12066356	0.88[ASN][1000 genomes]
rs12096035	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12722832	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12726409	0.87[EUR][1000 genomes]
rs12727947	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12728266	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12730098	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12736502	0.87[EUR][1000 genomes]
rs12737825	0.85[EUR][1000 genomes]
rs12743785	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12745269	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746203	0.81[EUR][1000 genomes]
rs12747025	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12756678	0.87[EUR][1000 genomes]
rs1470390	0.87[EUR][1000 genomes]
rs1493600	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1530451	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17721302	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120770	0.87[EUR][1000 genomes]
rs2358448	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358454	0.85[EUR][1000 genomes]
rs2884465	0.82[EUR][1000 genomes]
rs2884466	0.80[EUR][1000 genomes]
rs34080686	0.86[EUR][1000 genomes]
rs34212128	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34244392	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34447409	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34515259	0.86[EUR][1000 genomes]
rs34740542	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35556190	0.84[EUR][1000 genomes]
rs35872305	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661987	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518399	0.87[EUR][1000 genomes]
rs7521041	0.88[ASN][1000 genomes]
rs7531219	0.88[ASN][1000 genomes]
rs968531	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968532	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv3442043	chr1:212457854-212460702	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55814152	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs55814152	RP11-15I11.3	cis	lung	GTEx
rs55814152	RP11-15I11.3	cis	Thyroid	GTEx
rs55814152	RP11-15I11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212457000-212461400	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:212457000-212461600	Active TSS	Colonic Mucosa	Colon
3	chr1:212457200-212460800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:212457200-212460800	Active TSS	Pancreas	Pancrea
5	chr1:212457200-212461000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:212457200-212461000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:212457200-212461600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:212457200-212461600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:212457400-212461000	Active TSS	Stomach Mucosa	stomach
10	chr1:212457400-212461400	Active TSS	Fetal Intestine Large	intestine
11	chr1:212457400-212461800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:212457400-212463400	Active TSS	Right Ventricle	heart
13	chr1:212457600-212460800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:212457600-212460800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:212457600-212460800	Active TSS	Brain Anterior Caudate	brain
16	chr1:212457600-212461400	Active TSS	Left Ventricle	heart
17	chr1:212457600-212461600	Active TSS	NHDF-Ad	bronchial
18	chr1:212457600-212461800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:212457600-212461800	Active TSS	Esophagus	oesophagus
20	chr1:212457600-212462400	Active TSS	Aorta	Aorta
21	chr1:212457600-212462800	Active TSS	Psoas Muscle	Psoas
22	chr1:212457800-212460800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:212457800-212460800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:212457800-212460800	Active TSS	Brain Angular Gyrus	brain
25	chr1:212457800-212460800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:212457800-212460800	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr1:212457800-212460800	Active TSS	Small Intestine	intestine
28	chr1:212457800-212461000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:212457800-212461000	Active TSS	A549	lung
30	chr1:212457800-212461600	Active TSS	Lung	lung
31	chr1:212457800-212461600	Active TSS	GM12878-XiMat	blood
32	chr1:212457800-212461800	Active TSS	Gastric	stomach
33	chr1:212458000-212460800	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:212458000-212460800	Active TSS	Colon Smooth Muscle	Colon
35	chr1:212458000-212460800	Active TSS	NHEK	skin
36	chr1:212458000-212461000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:212458000-212461000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:212458000-212461400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:212458000-212461400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:212458000-212461400	Active TSS	Liver	Liver
41	chr1:212458000-212461400	Active TSS	Fetal Intestine Small	intestine
42	chr1:212458000-212461400	Active TSS	Ovary	ovary
43	chr1:212458000-212461400	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:212458000-212461600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:212458000-212461600	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:212458000-212461600	Active TSS	Hela-S3	cervix
47	chr1:212458000-212461800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:212458000-212463400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:212458200-212460800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:212458200-212460800	Active TSS	Stomach Smooth Muscle	stomach

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