Variant report

Variant	rs2867296
Chromosome Location	chr1:150903234-150903235
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150897904..150900695-chr1:150901454..150905304,5	K562	blood:
2	chr1:150902864..150904441-chr1:150906558..150909228,2	K562	blood:

Variant related genes	Relation type
ENSG00000143379	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1027699	0.85[EUR][1000 genomes]
rs10305664	0.85[EUR][1000 genomes]
rs10305672	0.87[EUR][1000 genomes]
rs10305673	0.85[EUR][1000 genomes]
rs10305704	0.85[EUR][1000 genomes]
rs10305711	0.85[EUR][1000 genomes]
rs10305714	0.85[EUR][1000 genomes]
rs10399947	0.86[EUR][1000 genomes]
rs10888397	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888398	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204733	0.84[EUR][1000 genomes]
rs11204739	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204742	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204743	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204747	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204748	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204749	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204750	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11552229	0.85[EUR][1000 genomes]
rs11579736	0.83[EUR][1000 genomes]
rs11581757	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11582281	0.84[EUR][1000 genomes]
rs11583707	0.85[EUR][1000 genomes]
rs11589458	0.85[EUR][1000 genomes]
rs11589886	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12059949	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12067685	0.84[EUR][1000 genomes]
rs12075597	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12090215	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12096831	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12097963	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405726	0.80[EUR][1000 genomes]
rs12409208	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12410394	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12410869	0.80[EUR][1000 genomes]
rs12562939	0.84[EUR][1000 genomes]
rs1546376	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17660092	0.85[EUR][1000 genomes]
rs1889741	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1972060	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2004903	0.86[ASN][1000 genomes]
rs2089082	0.85[EUR][1000 genomes]
rs2124952	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271076	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272214	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280627	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864882	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867297	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34985895	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3768015	0.85[EUR][1000 genomes]
rs3768016	0.85[EUR][1000 genomes]
rs3843843	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3849279	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4451553	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970928	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970929	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970930	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970931	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970980	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4970982	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970984	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970985	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970986	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970987	0.85[EUR][1000 genomes]
rs4970988	0.85[EUR][1000 genomes]
rs57818453	0.80[EUR][1000 genomes]
rs59024312	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587542	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658066	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6660845	0.87[EUR][1000 genomes]
rs6669855	0.86[EUR][1000 genomes]
rs6677420	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66847267	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686064	0.83[ASN][1000 genomes]
rs6692228	0.82[ASN][1000 genomes]
rs72704652	0.85[EUR][1000 genomes]
rs72704654	0.85[EUR][1000 genomes]
rs72704658	0.84[EUR][1000 genomes]
rs72704679	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72704682	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72704685	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7518156	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521592	0.85[EUR][1000 genomes]
rs752376	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528773	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7556451	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556661	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8444	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs897815	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9661876	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2867296	RP11-316M1.12	cis	Artery Tibial	GTEx
rs2867296	RP11-316M1.12	cis	Artery Aorta	GTEx
rs2867296	RP11-316M1.12	cis	Whole Blood	GTEx
rs2867296	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs2867296	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs2867296	GOLPH3L	cis	Nerve Tibial	GTEx
rs2867296	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs2867296	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs2867296	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs2867296	RP11-316M1.12	cis	Thyroid	GTEx
rs2867296	CTSS	cis	Thyroid	GTEx
rs2867296	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs2867296	CTSS	cis	Artery Tibial	GTEx
rs2867296	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2867296	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs2867296	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs2867296	HORMAD1	cis	Nerve Tibial	GTEx
rs2867296	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs2867296	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs2867296	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs2867296	HORMAD1	cis	Esophagus Mucosa	GTEx
rs2867296	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2867296	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs2867296	RP11-316M1.12	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150899400-150915000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:150899600-150913200	Weak transcription	Aorta	Aorta
3	chr1:150899600-150913200	Weak transcription	Right Ventricle	heart
4	chr1:150899600-150913600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:150899600-150943400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:150900000-150903400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:150900000-150904200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:150900000-150905400	Strong transcription	NHDF-Ad	bronchial
9	chr1:150900000-150905600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:150900000-150905600	Strong transcription	Osteobl	bone
11	chr1:150900000-150905800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:150900000-150906200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:150900000-150913400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:150900000-150915200	Weak transcription	Esophagus	oesophagus
15	chr1:150900200-150903400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:150900200-150903400	Strong transcription	Fetal Intestine Large	intestine
17	chr1:150900200-150903400	Strong transcription	Fetal Lung	lung
18	chr1:150900200-150903400	Strong transcription	Ovary	ovary
19	chr1:150900200-150903400	Strong transcription	Thymus	Thymus
20	chr1:150900200-150903600	Strong transcription	Colonic Mucosa	Colon
21	chr1:150900200-150904200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:150900200-150904200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:150900200-150904200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:150900200-150904200	Strong transcription	A549	lung
25	chr1:150900200-150904600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:150900200-150905200	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr1:150900200-150905600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:150900200-150905800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:150900200-150905800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr1:150900200-150906000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:150900200-150906000	Strong transcription	Fetal Kidney	kidney
32	chr1:150900200-150906000	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:150900200-150906200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:150900200-150906200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:150900200-150906600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr1:150900200-150908400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:150900200-150909000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:150900200-150941800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:150900400-150903600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr1:150900400-150903600	Strong transcription	HMEC	breast
41	chr1:150900400-150903600	Strong transcription	HSMMtube	muscle
42	chr1:150900400-150903600	Strong transcription	NHEK	skin
43	chr1:150900400-150903800	Strong transcription	Adipose Nuclei	Adipose
44	chr1:150900400-150904000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:150900400-150904000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:150900400-150904000	Strong transcription	Brain Anterior Caudate	brain
47	chr1:150900400-150904000	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:150900400-150904200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:150900400-150904400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:150900400-150904600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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