Variant report

Variant	rs4509581
Chromosome Location	chr1:150774465-150774466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150550318..150552740-chr1:150773930..150776202,2	MCF-7	breast:
2	chr1:150772986..150774587-chr1:150774914..150777636,2	K562	blood:
3	chr1:150550459..150552854-chr1:150773382..150778382,4	MCF-7	breast:
4	chr1:150773328..150775046-chr1:150777783..150780763,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143387	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1027699	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10305664	0.81[AFR][1000 genomes]
rs10305673	0.81[AFR][1000 genomes]
rs10305704	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10305711	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10305714	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes]
rs10305720	0.81[EUR][1000 genomes]
rs10788792	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10788794	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10888391	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10888392	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10888393	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10888394	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888395	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888397	0.83[CEU][hapmap]
rs10888398	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs11204691	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11204697	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11204698	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11204704	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11204722	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11204723	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204726	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204733	0.81[AFR][1000 genomes]
rs11204749	0.86[CEU][hapmap]
rs1136808	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11552229	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11581757	0.83[CEU][hapmap]
rs11582281	0.81[AFR][1000 genomes]
rs11586422	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11587444	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11589458	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11800855	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11803569	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11803940	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11804276	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11807409	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11807450	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12063547	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12068264	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12072339	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12085336	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12086472	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12089989	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12402939	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12403255	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12404949	0.83[AFR][1000 genomes]
rs12409208	0.83[CEU][hapmap]
rs12410869	0.95[CEU][hapmap]
rs1336899	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1336900	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1415148	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1532770	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16827671	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17658705	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs17660092	0.83[AFR][1000 genomes]
rs1889740	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1889741	0.95[CEU][hapmap]
rs2089082	0.83[AFR][1000 genomes]
rs2124952	0.83[CEU][hapmap]
rs2184833	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2228099	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2230061	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2256355	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2272214	0.83[CEU][hapmap]
rs2275235	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2275236	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2280078	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2280627	0.96[CEU][hapmap]
rs2864869	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2864871	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2864873	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864882	0.81[EUR][1000 genomes]
rs2867301	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2867302	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3754212	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3768005	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3768013	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3768015	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3768016	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3768018	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3849279	0.95[CEU][hapmap]
rs4319334	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537557	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970984	0.81[EUR][1000 genomes]
rs4970985	0.81[EUR][1000 genomes]
rs4970987	0.83[CEU][hapmap]
rs4970988	0.83[CEU][hapmap]
rs57818453	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59337856	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587516	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6587518	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6657388	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6660084	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6660845	0.81[AFR][1000 genomes]
rs6661415	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6671737	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6678013	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs66847267	0.81[EUR][1000 genomes]
rs6693120	0.83[ASN][1000 genomes]
rs6700022	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs72704652	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72704654	0.83[AFR][1000 genomes]
rs72704656	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72704658	0.80[EUR][1000 genomes]
rs7412396	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7418501	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7511673	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7514004	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7521592	0.81[ASN][1000 genomes]
rs7521898	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs752376	0.95[CEU][hapmap]
rs7524620	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7526489	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7529194	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7532045	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7538493	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7540874	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7556661	0.83[CEU][hapmap]
rs8444	0.83[CEU][hapmap]
rs868751	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs897815	0.83[CEU][hapmap]
rs951281	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[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	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs4509581	ARNT	cis	uninvolved skin	skin_eQTL
rs4509581	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs4509581	HORMAD1	cis	lesional skin	skin_eQTL
rs4509581	RP11-316M1.12	cis	Artery Tibial	GTEx
rs4509581	RP11-316M1.12	cis	lung	GTEx
rs4509581	HORMAD1	cis	Nerve Tibial	GTEx
rs4509581	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs4509581	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs4509581	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs4509581	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs4509581	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs4509581	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs4509581	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs4509581	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs4509581	HORMAD1	cis	normal skin	skin_eQTL
rs4509581	ARNT	cis	normal skin	skin_eQTL
rs4509581	CTSS	cis	Artery Tibial	GTEx
rs4509581	HORMAD1	cis	Esophagus Mucosa	GTEx
rs4509581	RP11-316M1.12	cis	Whole Blood	GTEx
rs4509581	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs4509581	CTSS	cis	multi-tissue	Pritchard
rs4509581	RP11-316M1.12	cis	Artery Aorta	GTEx
rs4509581	CTSK	cis	multi-tissue	Pritchard
rs4509581	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs4509581	ARNT	cis	lesional skin	skin_eQTL
rs4509581	HORMAD1	cis	uninvolved skin	skin_eQTL
rs4509581	CTSS	cis	Thyroid	GTEx
rs4509581	GOLPH3L	cis	Nerve Tibial	GTEx
rs4509581	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs4509581	RP11-316M1.12	cis	Thyroid	GTEx
rs4509581	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs4509581	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150760600-150779600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:150761200-150783200	Weak transcription	GM12878-XiMat	blood
3	chr1:150762400-150779200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:150762400-150780000	Weak transcription	NHEK	skin
5	chr1:150764600-150781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:150765400-150781400	Weak transcription	HMEC	breast
7	chr1:150765400-150793600	Weak transcription	Fetal Heart	heart
8	chr1:150766800-150775800	Weak transcription	HUVEC	blood vessel
9	chr1:150767000-150779400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:150767200-150779400	Weak transcription	Fetal Brain Male	brain
11	chr1:150767600-150783600	Weak transcription	Psoas Muscle	Psoas
12	chr1:150767800-150777000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:150767800-150778400	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:150767800-150780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:150768000-150776600	Strong transcription	Placenta	Placenta
16	chr1:150768000-150777000	Strong transcription	Liver	Liver
17	chr1:150768200-150784000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:150769400-150785200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:150770000-150781600	Weak transcription	HSMMtube	muscle
20	chr1:150770400-150778400	Weak transcription	Gastric	stomach
21	chr1:150770400-150783400	Weak transcription	Stomach Mucosa	stomach
22	chr1:150770600-150779200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:150770600-150779600	Weak transcription	Fetal Thymus	thymus
24	chr1:150770600-150783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:150770800-150780600	Weak transcription	Esophagus	oesophagus
26	chr1:150771200-150784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:150771200-150785400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:150771400-150775400	Weak transcription	K562	blood
29	chr1:150771400-150783000	Weak transcription	Brain Germinal Matrix	brain
30	chr1:150771600-150785200	Weak transcription	Pancreas	Pancrea
31	chr1:150771800-150778200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:150771800-150779200	Weak transcription	Fetal Lung	lung
33	chr1:150771800-150783600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:150771800-150783600	Weak transcription	A549	lung
35	chr1:150772000-150778400	Weak transcription	Colonic Mucosa	Colon
36	chr1:150772000-150779400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:150772000-150780600	Weak transcription	Fetal Brain Female	brain
38	chr1:150772200-150774800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:150772200-150774800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:150772200-150775200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:150772200-150775400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:150772200-150777400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:150772200-150778200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:150772200-150778400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:150772200-150778400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:150772200-150779000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:150772200-150779000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:150772200-150779000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:150772200-150779000	Weak transcription	Thymus	Thymus
50	chr1:150772200-150779400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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