Variant report

Variant	rs11265238
Chromosome Location	chr1:154149767-154149768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
2	chr1:154142747..154146273-chr1:154146772..154152940,5	K562	blood:
3	chr1:153961855..153964878-chr1:154149314..154153044,5	K562	blood:
4	chr1:154138203..154141121-chr1:154149226..154151416,2	MCF-7	breast:
5	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
6	chr1:154148286..154150697-chr1:154192561..154194921,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000264384	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158820	0.91[JPT][hapmap]
rs1044013	0.91[JPT][hapmap]
rs1113142	0.88[YRI][hapmap]
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];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1194593	0.91[JPT][hapmap]
rs1194596	0.91[JPT][hapmap]
rs1194601	0.80[YRI][hapmap]
rs12025237	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs12026177	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12026615	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12027999	0.83[EUR][1000 genomes]
rs12028949	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs12062977	0.91[JPT][hapmap]
rs12733060	0.83[EUR][1000 genomes]
rs12738393	0.82[EUR][1000 genomes]
rs12745098	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16835846	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16835852	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16835909	0.84[YRI][hapmap]
rs1685625	0.88[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];0.83[EUR][1000 genomes]
rs2340473	0.86[JPT][hapmap]
rs2633434	0.80[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs28372838	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2879788	0.91[JPT][hapmap]
rs3002660	0.80[EUR][1000 genomes]
rs34128679	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34335016	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35761479	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762340	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs3790613	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3790614	0.83[EUR][1000 genomes]
rs3811453	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs3811455	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]
rs3828077	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3935419	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4433384	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs4620534	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60282844	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6427509	0.91[JPT][hapmap]
rs6666943	0.88[YRI][hapmap]
rs6673752	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs6676022	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719	0.91[JPT][hapmap]
rs715737	0.88[YRI][hapmap]
rs9803857	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11265238	HAX1	cis	lymphoblastoid	seeQTL
rs11265238	HAX1	cis	cerebellum	SCAN
rs11265238	RAB13	cis	parietal	SCAN
rs11265238	SLC27A3	cis	lymphoblastoid	seeQTL
rs11265238	PIP5K1A	cis	cerebellum	SCAN
rs11265238	C1orf43	cis	parietal	SCAN
rs11265238	SCAMP3	cis	parietal	SCAN
rs11265238	HAX1	cis	parietal	SCAN
rs11265238	DENND4B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154127800-154150000	Strong transcription	H1 Cell Line	embryonic stem cell
2	chr1:154128000-154150400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:154128000-154150800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:154128200-154150200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:154128200-154151200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:154129600-154149800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:154129600-154150400	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr1:154130200-154150600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:154130600-154149800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:154130600-154150000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:154133200-154149800	Strong transcription	Thymus	Thymus
12	chr1:154133600-154149800	Strong transcription	Dnd41	blood
13	chr1:154133600-154150200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:154142400-154152000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:154143800-154153600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:154144200-154154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:154145600-154150600	Weak transcription	Aorta	Aorta
18	chr1:154145800-154150000	Weak transcription	Right Ventricle	heart
19	chr1:154145800-154150200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:154145800-154150200	Weak transcription	Fetal Brain Male	brain
21	chr1:154145800-154150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:154145800-154150200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:154145800-154150600	Weak transcription	Ovary	ovary
24	chr1:154145800-154151200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:154145800-154153400	Weak transcription	Fetal Kidney	kidney
26	chr1:154146800-154151000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:154147000-154151400	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr1:154147200-154149800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:154147200-154152400	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr1:154147800-154152400	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:154148000-154149800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:154148000-154150600	Genic enhancers	Primary B cells from cord blood	blood
33	chr1:154148000-154150800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:154148200-154150200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:154148200-154150200	Genic enhancers	Duodenum Mucosa	Duodenum
36	chr1:154148200-154150800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:154148200-154151000	Enhancers	Colonic Mucosa	Colon
38	chr1:154148200-154153800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:154148400-154149800	Weak transcription	Fetal Heart	heart
40	chr1:154148400-154151000	Genic enhancers	Fetal Intestine Large	intestine
41	chr1:154148400-154151200	Enhancers	Small Intestine	intestine
42	chr1:154148400-154152400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:154148400-154152800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:154148400-154152800	Genic enhancers	Fetal Thymus	thymus
45	chr1:154148400-154153000	Genic enhancers	Fetal Muscle Leg	muscle
46	chr1:154148600-154149800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:154148600-154150000	Genic enhancers	K562	blood
48	chr1:154148600-154150400	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr1:154148600-154150600	Genic enhancers	Hela-S3	cervix
50	chr1:154148600-154150800	Weak transcription	Fetal Lung	lung

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