Variant report

Variant	rs7514004
Chromosome Location	chr1:150818234-150818235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150816940..150818547-chr1:150824662..150826760,2	MCF-7	breast:
2	chr1:150818101..150820451-chr1:150845957..150847581,2	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1027699	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305664	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10305667	0.82[ASN][1000 genomes]
rs10305672	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305673	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305704	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305711	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305714	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305720	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10399947	0.89[EUR][1000 genomes]
rs10788794	0.88[EUR][1000 genomes]
rs10888391	0.88[EUR][1000 genomes]
rs10888392	0.89[EUR][1000 genomes]
rs10888393	0.83[EUR][1000 genomes]
rs10888394	0.90[EUR][1000 genomes]
rs10888395	0.92[EUR][1000 genomes]
rs10888397	0.85[EUR][1000 genomes]
rs10888398	0.91[EUR][1000 genomes]
rs11204722	0.88[EUR][1000 genomes]
rs11204723	0.82[EUR][1000 genomes]
rs11204726	0.90[EUR][1000 genomes]
rs11204733	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204739	0.86[EUR][1000 genomes]
rs11204742	0.84[EUR][1000 genomes]
rs11204747	0.85[EUR][1000 genomes]
rs11204748	0.84[EUR][1000 genomes]
rs11204749	0.85[EUR][1000 genomes]
rs11552229	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581757	0.85[EUR][1000 genomes]
rs11582281	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11589458	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589886	0.87[EUR][1000 genomes]
rs11800855	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12068264	0.81[EUR][1000 genomes]
rs12075597	0.87[EUR][1000 genomes]
rs12085336	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12090215	0.85[EUR][1000 genomes]
rs12096831	0.87[EUR][1000 genomes]
rs12097963	0.86[EUR][1000 genomes]
rs12406660	0.82[ASN][1000 genomes]
rs12409208	0.87[EUR][1000 genomes]
rs12410394	0.87[EUR][1000 genomes]
rs12410869	0.94[EUR][1000 genomes]
rs1532770	0.87[EUR][1000 genomes]
rs16827671	0.90[EUR][1000 genomes]
rs17660092	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889740	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889741	0.93[EUR][1000 genomes]
rs1972060	0.84[EUR][1000 genomes]
rs2089082	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228099	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2230061	0.81[EUR][1000 genomes]
rs2256355	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271076	0.86[EUR][1000 genomes]
rs2275235	0.82[EUR][1000 genomes]
rs2280627	0.84[EUR][1000 genomes]
rs2864869	0.82[EUR][1000 genomes]
rs2864871	0.81[ASN][1000 genomes]
rs2864873	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2864882	0.91[EUR][1000 genomes]
rs2867297	0.86[EUR][1000 genomes]
rs36008098	0.93[EUR][1000 genomes]
rs3754212	0.83[EUR][1000 genomes]
rs3768013	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768015	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768016	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768018	0.88[EUR][1000 genomes]
rs3849279	0.82[EUR][1000 genomes]
rs4319334	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4509581	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4537557	0.82[EUR][1000 genomes]
rs4970928	0.81[EUR][1000 genomes]
rs4970930	0.84[EUR][1000 genomes]
rs4970931	0.86[EUR][1000 genomes]
rs4970980	0.94[EUR][1000 genomes]
rs4970982	0.87[EUR][1000 genomes]
rs4970984	0.91[EUR][1000 genomes]
rs4970985	0.91[EUR][1000 genomes]
rs57818453	0.85[EUR][1000 genomes]
rs59337856	0.90[EUR][1000 genomes]
rs6587542	0.86[EUR][1000 genomes]
rs6657388	0.83[EUR][1000 genomes]
rs6660084	0.90[EUR][1000 genomes]
rs6660845	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669855	0.89[EUR][1000 genomes]
rs6671737	0.83[EUR][1000 genomes]
rs66847267	0.91[EUR][1000 genomes]
rs6686064	0.86[EUR][1000 genomes]
rs72704639	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704652	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704654	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704656	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704658	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704679	0.89[EUR][1000 genomes]
rs72704682	0.82[EUR][1000 genomes]
rs72704685	0.81[EUR][1000 genomes]
rs7518156	0.81[EUR][1000 genomes]
rs7521592	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752376	0.82[EUR][1000 genomes]
rs7526489	0.81[EUR][1000 genomes]
rs7532045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556451	0.85[EUR][1000 genomes]
rs7556661	0.85[EUR][1000 genomes]
rs897815	0.84[EUR][1000 genomes]
rs9661876	0.86[EUR][1000 genomes]

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	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	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
4	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
5	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1010875	chr1:150796816-150845827	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv1793983	chr1:150804748-150825924	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs7514004	HORMAD1	cis	Nerve Tibial	GTEx
rs7514004	GOLPH3L	cis	Nerve Tibial	GTEx
rs7514004	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs7514004	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs7514004	RP11-316M1.12	cis	Artery Aorta	GTEx
rs7514004	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs7514004	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs7514004	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs7514004	CTSS	cis	Thyroid	GTEx
rs7514004	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs7514004	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs7514004	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs7514004	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs7514004	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs7514004	RP11-316M1.12	cis	Whole Blood	GTEx
rs7514004	RP11-316M1.12	cis	Thyroid	GTEx
rs7514004	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs7514004	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs7514004	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs7514004	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs7514004	RP11-316M1.12	cis	Artery Tibial	GTEx
rs7514004	RP11-316M1.12	cis	lung	GTEx
rs7514004	HORMAD1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150793200-150823200	Strong transcription	Placenta	Placenta
2	chr1:150801800-150818600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:150801800-150824600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:150805800-150824600	Weak transcription	HMEC	breast
5	chr1:150807200-150820800	Weak transcription	Spleen	Spleen
6	chr1:150807400-150824600	Weak transcription	A549	lung
7	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
8	chr1:150808000-150821600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
10	chr1:150809000-150819200	Weak transcription	K562	blood
11	chr1:150809000-150823000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:150809000-150824400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:150809000-150824600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:150809200-150820600	Weak transcription	Brain Germinal Matrix	brain
15	chr1:150809200-150824600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:150809400-150821000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:150809400-150821000	Weak transcription	Thymus	Thymus
19	chr1:150809400-150823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:150809600-150820400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
22	chr1:150810000-150824800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:150810200-150824600	Weak transcription	NHLF	lung
24	chr1:150810400-150846600	Weak transcription	Fetal Heart	heart
25	chr1:150812000-150824400	Weak transcription	Fetal Brain Male	brain
26	chr1:150812000-150831200	Weak transcription	Lung	lung
27	chr1:150812000-150847000	Weak transcription	Gastric	stomach
28	chr1:150812200-150821600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:150812200-150822200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:150812200-150824600	Weak transcription	HepG2	liver
31	chr1:150812200-150824600	Weak transcription	NHEK	skin
32	chr1:150812200-150828000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:150812200-150829800	Weak transcription	HUVEC	blood vessel
34	chr1:150812200-150834000	Weak transcription	Brain Angular Gyrus	brain
35	chr1:150812400-150818400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:150812400-150818600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:150812400-150818800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:150812400-150819000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:150812400-150819200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:150812400-150819200	Weak transcription	HSMMtube	muscle
41	chr1:150812400-150819400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:150812400-150820000	Weak transcription	Brain Anterior Caudate	brain
43	chr1:150812400-150820000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:150812400-150820600	Weak transcription	Aorta	Aorta
45	chr1:150812400-150820600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:150812400-150821600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:150812400-150824400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:150812400-150824400	Weak transcription	Dnd41	blood
49	chr1:150812400-150824400	Weak transcription	GM12878-XiMat	blood
50	chr1:150812400-150824600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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