Variant report

Variant	rs7534162
Chromosome Location	chr1:155065159-155065160
allele	A/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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155064094..155065891-chr1:155117626..155119134,2	MCF-7	breast:
2	chr1:155056065..155060440-chr1:155062354..155065779,6	K562	blood:
3	chr1:155063588..155065472-chr1:155139784..155141178,19	K562	blood:
4	chr1:155063960..155065905-chr1:155106879..155109737,2	K562	blood:
5	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
6	chr1:155064687..155066465-chr1:155098268..155100764,2	K562	blood:
7	chr1:155063197..155065569-chr1:155078354..155080513,2	K562	blood:
8	chr1:155062448..155069217-chr1:155142816..155147773,12	MCF-7	breast:
9	chr1:155055416..155060440-chr1:155063419..155068026,8	K562	blood:
10	chr1:155064469..155067923-chr1:155161991..155164572,4	MCF-7	breast:
11	chr1:155063776..155066689-chr1:155134444..155136393,2	MCF-7	breast:
12	chr1:155063703..155067297-chr1:155143302..155147272,4	K562	blood:
13	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
14	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:
15	chr1:155051153..155052949-chr1:155062882..155065353,2	K562	blood:
16	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:
17	chr1:155064648..155066932-chr1:155147928..155150182,2	K562	blood:
18	chr1:155062611..155066935-chr1:155144495..155147775,5	MCF-7	breast:
19	chr1:155064464..155066465-chr1:155098268..155100764,3	K562	blood:
20	chr1:155063203..155065869-chr1:155133125..155134696,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202027	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000179085	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10796938	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10796939	0.90[ASN][1000 genomes]
rs10908454	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908455	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908456	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264312	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264313	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264318	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11264321	1.00[ASN][1000 genomes]
rs11264322	0.97[ASN][1000 genomes]
rs11264327	0.93[ASN][1000 genomes]
rs11264328	0.93[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11581730	0.87[AMR][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.97[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	1.00[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12145362	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870939	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306124	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	0.95[ASN][1000 genomes]
rs4361977	1.00[ASN][1000 genomes]
rs4625273	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845706	0.83[EUR][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7366138	0.95[ASN][1000 genomes]
rs7366355	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7367207	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7367758	0.97[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9297	0.85[JPT][hapmap]
rs9330263	0.88[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	esv2762194	chr1:155063145-155067283	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7534162	S100A3	cis	parietal	SCAN
rs7534162	SPRR4	cis	parietal	SCAN
rs7534162	EFNA1	cis	cerebellum	SCAN
rs7534162	SMCP	cis	cerebellum	SCAN
rs7534162	RPRD2	cis	parietal	SCAN
rs7534162	BOLA1	cis	parietal	SCAN
rs7534162	CRNN	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155058600-155066000	Weak transcription	Right Atrium	heart
2	chr1:155059000-155066200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:155059200-155066600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:155059400-155065600	Weak transcription	Fetal Lung	lung
5	chr1:155059600-155065600	Weak transcription	Spleen	Spleen
6	chr1:155059800-155066400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:155063400-155067200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:155063600-155067200	Enhancers	Right Ventricle	heart
9	chr1:155064000-155066000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:155064200-155065200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:155064200-155065800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:155064200-155066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:155064200-155066200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:155064200-155066600	Weak transcription	GM12878-XiMat	blood
15	chr1:155064400-155065200	Weak transcription	Fetal Brain Male	brain
16	chr1:155064400-155065400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:155064400-155065400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:155064400-155065600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:155064400-155065800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:155064400-155065800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:155064400-155065800	Weak transcription	Brain Substantia Nigra	brain
22	chr1:155064400-155065800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:155064400-155065800	Weak transcription	Fetal Heart	heart
24	chr1:155064400-155065800	Weak transcription	Ovary	ovary
25	chr1:155064400-155066000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:155064400-155066000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:155064400-155066000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:155064400-155066000	Weak transcription	Colonic Mucosa	Colon
29	chr1:155064400-155066000	Weak transcription	Lung	lung
30	chr1:155064400-155066000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:155064400-155066200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:155064400-155066200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:155064400-155066200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:155064400-155066200	Weak transcription	Adipose Nuclei	Adipose
35	chr1:155064400-155066200	Weak transcription	Esophagus	oesophagus
36	chr1:155064400-155066200	Weak transcription	Fetal Brain Female	brain
37	chr1:155064400-155066200	Weak transcription	Fetal Intestine Large	intestine
38	chr1:155064400-155066200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:155064400-155066200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:155064400-155066200	Weak transcription	Hela-S3	cervix
41	chr1:155064400-155066400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:155064400-155066400	Weak transcription	Fetal Thymus	thymus
43	chr1:155064400-155066400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:155064400-155066400	Weak transcription	HSMM	muscle
45	chr1:155064400-155066600	Weak transcription	Stomach Mucosa	stomach
46	chr1:155064400-155066800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:155064600-155065800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:155064600-155066000	Weak transcription	Liver	Liver
49	chr1:155064600-155066000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:155064600-155066000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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