Variant report

Variant	rs10305672
Chromosome Location	chr1:150825630-150825631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150825294..150827430-chr1:150885825..150887706,2	MCF-7	breast:
2	chr1:150824595..150826389-chr1:150944188..150947184,2	K562	blood:
3	chr1:150824355..150826588-chr1:150896874..150898598,2	MCF-7	breast:
4	chr1:150824402..150827386-chr1:150847961..150849827,2	MCF-7	breast:
5	chr1:150816940..150818547-chr1:150824662..150826760,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231073	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1027699	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305664	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10305667	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10305673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305704	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305711	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305714	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305720	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10399947	0.90[EUR][1000 genomes]
rs10888392	0.82[EUR][1000 genomes]
rs10888393	0.88[EUR][1000 genomes]
rs10888394	0.81[EUR][1000 genomes]
rs10888395	0.84[EUR][1000 genomes]
rs10888397	0.89[EUR][1000 genomes]
rs10888398	0.82[EUR][1000 genomes]
rs11204723	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11204726	0.81[EUR][1000 genomes]
rs11204733	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204739	0.91[EUR][1000 genomes]
rs11204742	0.88[EUR][1000 genomes]
rs11204750	0.86[EUR][1000 genomes]
rs11552229	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11581757	0.89[EUR][1000 genomes]
rs11582281	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11589458	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11589886	0.82[EUR][1000 genomes]
rs11800855	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12059949	0.86[EUR][1000 genomes]
rs12068264	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12085336	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12090215	0.89[EUR][1000 genomes]
rs12096831	0.92[EUR][1000 genomes]
rs12097963	0.91[EUR][1000 genomes]
rs12406660	0.82[ASN][1000 genomes]
rs12409208	0.92[EUR][1000 genomes]
rs12410394	0.92[EUR][1000 genomes]
rs12410869	0.84[EUR][1000 genomes]
rs1546376	0.86[EUR][1000 genomes]
rs16827671	0.81[EUR][1000 genomes]
rs17660092	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889740	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1889741	0.83[EUR][1000 genomes]
rs2089082	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2124952	0.87[EUR][1000 genomes]
rs2228099	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2230061	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2256355	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271076	0.81[EUR][1000 genomes]
rs2272214	0.87[EUR][1000 genomes]
rs2275235	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864869	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864871	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864873	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2864882	0.82[EUR][1000 genomes]
rs2867296	0.87[EUR][1000 genomes]
rs2867297	0.81[EUR][1000 genomes]
rs34985895	0.86[EUR][1000 genomes]
rs36008098	0.84[EUR][1000 genomes]
rs3754212	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3768013	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768015	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768016	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3843843	0.87[EUR][1000 genomes]
rs4451553	0.83[EUR][1000 genomes]
rs4537557	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4970928	0.85[EUR][1000 genomes]
rs4970929	0.84[EUR][1000 genomes]
rs4970930	0.88[EUR][1000 genomes]
rs4970931	0.81[EUR][1000 genomes]
rs4970980	0.84[EUR][1000 genomes]
rs4970982	0.92[EUR][1000 genomes]
rs4970984	0.82[EUR][1000 genomes]
rs4970985	0.82[EUR][1000 genomes]
rs4970986	0.88[EUR][1000 genomes]
rs57818453	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59024312	0.88[EUR][1000 genomes]
rs59337856	0.81[EUR][1000 genomes]
rs6587542	0.81[EUR][1000 genomes]
rs6657388	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6658066	0.84[EUR][1000 genomes]
rs6660084	0.81[EUR][1000 genomes]
rs6660845	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669855	0.90[EUR][1000 genomes]
rs6671737	0.88[EUR][1000 genomes]
rs6677420	0.82[EUR][1000 genomes]
rs66847267	0.82[EUR][1000 genomes]
rs6693120	0.85[EUR][1000 genomes]
rs72704639	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72704652	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704654	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72704656	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704658	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704679	0.82[EUR][1000 genomes]
rs72704682	0.90[EUR][1000 genomes]
rs72704685	0.90[EUR][1000 genomes]
rs7514004	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521592	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526489	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7528773	0.88[EUR][1000 genomes]
rs7532045	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556661	0.89[EUR][1000 genomes]
rs8444	0.86[EUR][1000 genomes]
rs897815	0.88[EUR][1000 genomes]
rs9661876	0.81[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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs10305672	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs10305672	CTSS	cis	Artery Tibial	GTEx
rs10305672	CTSS	cis	Thyroid	GTEx
rs10305672	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs10305672	RP11-316M1.12	cis	Artery Tibial	GTEx
rs10305672	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs10305672	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs10305672	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs10305672	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs10305672	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs10305672	RP11-316M1.12	cis	Artery Aorta	GTEx
rs10305672	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs10305672	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs10305672	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs10305672	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs10305672	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs10305672	RP11-316M1.12	cis	Thyroid	GTEx
rs10305672	HORMAD1	cis	Esophagus Mucosa	GTEx
rs10305672	GOLPH3L	cis	Nerve Tibial	GTEx
rs10305672	HORMAD1	cis	Nerve Tibial	GTEx
rs10305672	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs10305672	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs10305672	RP11-316M1.12	cis	lung	GTEx
rs10305672	RP11-316M1.12	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
2	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
3	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
5	chr1:150810400-150846600	Weak transcription	Fetal Heart	heart
6	chr1:150812000-150831200	Weak transcription	Lung	lung
7	chr1:150812000-150847000	Weak transcription	Gastric	stomach
8	chr1:150812200-150828000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:150812200-150829800	Weak transcription	HUVEC	blood vessel
10	chr1:150812200-150834000	Weak transcription	Brain Angular Gyrus	brain
11	chr1:150812400-150830800	Weak transcription	Ovary	ovary
12	chr1:150812400-150840600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:150812400-150842000	Weak transcription	Esophagus	oesophagus
14	chr1:150812400-150846800	Weak transcription	Fetal Kidney	kidney
15	chr1:150812600-150846000	Weak transcription	Small Intestine	intestine
16	chr1:150812600-150846800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:150814600-150833400	Weak transcription	Hela-S3	cervix
18	chr1:150814800-150839600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:150815200-150832000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:150815400-150825800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:150815400-150842400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:150815400-150846800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:150815600-150838000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:150816600-150829200	Weak transcription	HSMM	muscle
25	chr1:150817400-150827600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:150819600-150831200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:150820600-150846800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:150821200-150846600	Weak transcription	Aorta	Aorta
29	chr1:150821200-150846600	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:150821200-150846800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:150821200-150848600	Weak transcription	Spleen	Spleen
32	chr1:150822400-150827400	Weak transcription	Right Ventricle	heart
33	chr1:150822400-150827400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:150822400-150829600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:150822400-150846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:150822600-150826200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:150822800-150826600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:150823600-150826800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:150824000-150830600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:150824200-150827600	Strong transcription	Placenta	Placenta
41	chr1:150824200-150829400	Strong transcription	Fetal Stomach	stomach
42	chr1:150824200-150831000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:150824400-150826000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
44	chr1:150824400-150826600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr1:150824400-150826600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:150824400-150826800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr1:150824400-150827000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:150824400-150827000	ZNF genes & repeats	Dnd41	blood
49	chr1:150824400-150827000	ZNF genes & repeats	GM12878-XiMat	blood
50	chr1:150824400-150827400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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