Variant report

Variant	rs3811455
Chromosome Location	chr1:154164082-154164083
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154161897..154165113-chr1:154191510..154194039,3	K562	blood:
2	chr1:154162854..154164787-chr1:154165144..154168912,5	MCF-7	breast:
3	chr1:154163302..154165868-chr1:154226658..154229466,2	K562	blood:
4	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
5	chr1:154161421..154168420-chr1:154191340..154198003,13	MCF-7	breast:
6	chr1:154156233..154161758-chr1:154162933..154167291,6	K562	blood:
7	chr1:154163815..154166290-chr14:24587619..24590176,2	MCF-7	breast:
8	chr1:154154241..154157353-chr1:154161640..154168172,9	MCF-7	breast:
9	chr1:154163875..154165876-chr1:154529636..154532185,2	MCF-7	breast:
10	chr1:154162391..154165167-chr1:154243401..154246301,3	K562	blood:
11	chr1:154161694..154164323-chr1:154174873..154176615,2	MCF-7	breast:
12	chr1:153962483..153964703-chr1:154162511..154166249,3	MCF-7	breast:
13	chr1:154161792..154164519-chr1:154243896..154245592,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100897	Chromatin interaction
ENSG00000252817	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10158820	0.91[JPT][hapmap]
rs1044013	0.91[JPT][hapmap]
rs1113142	0.84[YRI][hapmap]
rs11265238	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265251	0.91[JPT][hapmap]
rs11265425	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11802893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194593	0.91[JPT][hapmap]
rs1194594	0.92[YRI][hapmap]
rs1194596	0.91[JPT][hapmap]
rs1194597	0.82[YRI][hapmap]
rs1194601	0.91[YRI][hapmap]
rs1194605	0.87[YRI][hapmap]
rs12025237	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs12026177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12026615	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12027999	0.87[EUR][1000 genomes]
rs12028949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs1205590	0.87[YRI][hapmap]
rs12062977	0.91[JPT][hapmap]
rs12733060	0.87[EUR][1000 genomes]
rs12738393	0.86[EUR][1000 genomes]
rs12745098	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16835846	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16835852	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1685625	0.80[YRI][hapmap]
rs1760802	0.91[JPT][hapmap]
rs2274993	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2340473	0.86[JPT][hapmap]
rs2500222	0.91[YRI][hapmap]
rs2633434	0.95[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs28372838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2879788	0.91[JPT][hapmap]
rs34128679	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34335016	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35761479	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762340	0.90[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs3790613	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs3790614	0.87[EUR][1000 genomes]
rs3811453	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs3828077	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs3935419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4433384	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs4620534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60282844	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6427509	0.91[JPT][hapmap]
rs6666943	0.84[YRI][hapmap]
rs6673752	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs6676022	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719	0.91[JPT][hapmap]
rs715737	0.84[YRI][hapmap]
rs9803857	0.91[JPT][hapmap]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3811455	HAX1	cis	parietal	SCAN
rs3811455	C1orf43	cis	parietal	SCAN
rs3811455	PIP5K1A	cis	cerebellum	SCAN
rs3811455	SCAMP3	cis	parietal	SCAN
rs3811455	HAX1	cis	cerebellum	SCAN
rs3811455	SLC27A3	cis	lymphoblastoid	seeQTL
rs3811455	HAX1	cis	lymphoblastoid	seeQTL
rs3811455	DENND4B	cis	parietal	SCAN
rs3811455	RAB13	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154156400-154164200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:154156600-154164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:154156800-154164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:154157200-154164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:154159000-154164600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:154159000-154184400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:154160200-154164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:154160400-154169400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:154160600-154164400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:154160600-154164400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:154160600-154164600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:154160800-154164400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:154160800-154164600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:154162600-154165200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:154162800-154164400	Enhancers	HUVEC	blood vessel
16	chr1:154162800-154164600	Active TSS	Right Atrium	heart
17	chr1:154162800-154164800	Active TSS	HSMMtube	muscle
18	chr1:154162800-154165000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:154163000-154164400	Active TSS	Fetal Muscle Trunk	muscle
20	chr1:154163000-154164400	Active TSS	Psoas Muscle	Psoas
21	chr1:154163000-154164400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:154163000-154165000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr1:154163000-154165400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:154163000-154166600	Enhancers	K562	blood
25	chr1:154163200-154164200	Enhancers	Ovary	ovary
26	chr1:154163200-154164400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
27	chr1:154163200-154166800	Enhancers	Pancreas	Pancrea
28	chr1:154163200-154169400	Weak transcription	Fetal Heart	heart
29	chr1:154163400-154164200	Enhancers	Osteobl	bone
30	chr1:154163400-154164400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:154163400-154164600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
32	chr1:154163600-154164200	Active TSS	Fetal Muscle Leg	muscle
33	chr1:154163600-154164200	Enhancers	Lung	lung
34	chr1:154163800-154164200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:154163800-154164600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:154163800-154166000	Weak transcription	Hela-S3	cervix
37	chr1:154163800-154178800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:154164000-154164200	Active TSS	HSMM	muscle
39	chr1:154164000-154165200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--

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