Variant report

Variant	rs1630905
Chromosome Location	chr12:123705330-123705331
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123704862..123707251-chr12:123716101..123718102,3	MCF-7	breast:
2	chr12:123702115..123705680-chr12:123713540..123715755,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1047158	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1051431	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10744147	0.87[EUR][1000 genomes]
rs10744148	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10744149	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10772993	0.91[EUR][1000 genomes]
rs10772995	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10772996	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10772998	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10773001	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10846478	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10846486	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10846487	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10846491	0.88[AMR][1000 genomes]
rs11057189	0.83[EUR][1000 genomes]
rs11057192	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11057204	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11057206	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11057210	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1106240	0.90[EUR][1000 genomes]
rs1106241	0.92[EUR][1000 genomes]
rs1260294	0.80[EUR][1000 genomes]
rs1270594	0.80[EUR][1000 genomes]
rs12817892	0.87[EUR][1000 genomes]
rs12818067	0.87[EUR][1000 genomes]
rs12829456	0.87[EUR][1000 genomes]
rs1402274	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1402275	0.89[AMR][1000 genomes]
rs1533703	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1569068	0.91[EUR][1000 genomes]
rs1615694	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1616131	0.91[EUR][1000 genomes]
rs1616181	0.91[EUR][1000 genomes]
rs1617156	0.85[EUR][1000 genomes]
rs1617434	0.92[EUR][1000 genomes]
rs1618679	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1621194	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1626899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1627724	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1630693	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1716156	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716157	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716158	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716159	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1716164	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716165	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716167	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716168	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716172	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1716173	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1716175	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716176	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716177	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716182	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716185	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727290	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1727294	0.91[EUR][1000 genomes]
rs1727296	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727300	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1727306	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1727309	0.93[EUR][1000 genomes]
rs1727310	0.93[EUR][1000 genomes]
rs1727313	0.89[EUR][1000 genomes]
rs1727314	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1727315	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1727316	0.91[EUR][1000 genomes]
rs1727317	0.89[EUR][1000 genomes]
rs1727318	0.87[EUR][1000 genomes]
rs1727319	0.84[EUR][1000 genomes]
rs1727320	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1727322	0.94[EUR][1000 genomes]
rs1727323	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1727324	0.96[EUR][1000 genomes]
rs1727325	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1727334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1790086	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790087	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790089	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1790090	0.93[EUR][1000 genomes]
rs1790095	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1790098	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1790099	0.87[AFR][1000 genomes]
rs1790100	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1790101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1790102	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1790108	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1790109	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1790116	0.91[EUR][1000 genomes]
rs1790120	0.82[EUR][1000 genomes]
rs1790123	0.93[EUR][1000 genomes]
rs1790124	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1790125	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790130	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1790131	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1969354	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1980252	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2049114	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2102949	0.82[EUR][1000 genomes]
rs2337934	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2510885	0.89[EUR][1000 genomes]
rs2682425	0.82[EUR][1000 genomes]
rs2682426	0.82[AMR][1000 genomes]
rs2682429	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2682433	0.97[EUR][1000 genomes]
rs2682434	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695476	0.97[EUR][1000 genomes]
rs2695478	0.96[EUR][1000 genomes]
rs2695479	0.93[EUR][1000 genomes]
rs2695480	0.97[EUR][1000 genomes]
rs2695481	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2695482	0.92[EUR][1000 genomes]
rs2851435	0.95[EUR][1000 genomes]
rs2851436	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851438	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851441	0.87[EUR][1000 genomes]
rs2851443	0.84[EUR][1000 genomes]
rs2851447	0.82[EUR][1000 genomes]
rs2851450	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2851451	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2947099	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2950537	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3018098	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34341465	0.87[EUR][1000 genomes]
rs4268544	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4372492	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4460848	0.83[EUR][1000 genomes]
rs4759371	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4759409	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4759415	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4759416	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4759417	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs58809476	0.87[EUR][1000 genomes]
rs7313483	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs884548	0.93[EUR][1000 genomes]
rs941305	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs941306	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs949142	0.93[EUR][1000 genomes]
rs9795522	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1630905	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1630905	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1630905	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1630905	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1630905	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1630905	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1630905	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1630905	SETD8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
2	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123654000-123707000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:123655000-123707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:123655000-123708000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:123674000-123706000	Weak transcription	HMEC	breast
13	chr12:123674600-123713400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:123678800-123706600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:123680600-123716600	Weak transcription	Colonic Mucosa	Colon
16	chr12:123684000-123707800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:123684000-123709800	Strong transcription	Liver	Liver
18	chr12:123685000-123708400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:123685400-123711600	Strong transcription	Fetal Stomach	stomach
20	chr12:123685800-123707200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:123686200-123707200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:123687200-123711600	Strong transcription	Fetal Intestine Small	intestine
23	chr12:123687800-123705800	Weak transcription	Small Intestine	intestine
24	chr12:123687800-123707000	Weak transcription	Right Ventricle	heart
25	chr12:123687800-123716600	Weak transcription	Gastric	stomach
26	chr12:123687800-123716600	Weak transcription	Pancreas	Pancrea
27	chr12:123687800-123717000	Weak transcription	Aorta	Aorta
28	chr12:123688000-123715200	Weak transcription	Fetal Heart	heart
29	chr12:123689600-123712200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:123690600-123710800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:123690800-123716000	Weak transcription	Psoas Muscle	Psoas
32	chr12:123694600-123716800	Weak transcription	Ovary	ovary
33	chr12:123694800-123705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:123696000-123706400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:123696000-123706800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:123696000-123706800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:123696200-123706600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:123696200-123707800	Strong transcription	Dnd41	blood
39	chr12:123696200-123708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:123696200-123709600	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:123696200-123715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:123696400-123706800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:123696400-123710400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:123696400-123710600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:123696400-123711600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr12:123698400-123707200	Strong transcription	Fetal Thymus	thymus
47	chr12:123698400-123716600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:123698600-123705800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:123698800-123706000	Weak transcription	Brain Substantia Nigra	brain
50	chr12:123698800-123707400	Weak transcription	Fetal Kidney	kidney

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