Variant report

Variant	rs12130734
Chromosome Location	chr1:93624374-93624375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93617900..93619477-chr1:93623441..93625211,2	K562	blood:
2	chr1:93623277..93625367-chr1:93644361..93646842,2	MCF-7	breast:
3	chr1:93621616..93625921-chr1:93644666..93648341,4	K562	blood:
4	chr1:93617900..93619581-chr1:93623441..93626747,4	K562	blood:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction
ENSG00000117500	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1000607	0.82[EUR][1000 genomes]
rs1057257	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060622	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10782955	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874759	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10874762	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874764	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874772	0.82[EUR][1000 genomes]
rs10874773	0.82[EUR][1000 genomes]
rs11164871	0.84[EUR][1000 genomes]
rs11164876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11164879	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164880	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164881	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164902	0.82[EUR][1000 genomes]
rs12030549	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038699	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12044657	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12118230	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12118262	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124011	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12128131	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12139009	0.87[EUR][1000 genomes]
rs12385720	0.81[EUR][1000 genomes]
rs1335679	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474927	0.82[EUR][1000 genomes]
rs1535699	0.81[EUR][1000 genomes]
rs1537758	0.94[ASN][1000 genomes]
rs1572343	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1856027	0.85[EUR][1000 genomes]
rs1932314	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1967721	0.96[ASN][1000 genomes]
rs2031225	0.81[EUR][1000 genomes]
rs2031226	0.81[EUR][1000 genomes]
rs2152358	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2208044	0.80[EUR][1000 genomes]
rs2295423	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2295424	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2297707	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2391254	0.82[EUR][1000 genomes]
rs2765545	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2783489	0.99[ASN][1000 genomes]
rs2783499	0.83[ASN][1000 genomes]
rs2783500	0.83[ASN][1000 genomes]
rs2783501	0.83[ASN][1000 genomes]
rs2783504	0.82[ASN][1000 genomes]
rs2815415	0.82[ASN][1000 genomes]
rs35940311	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4240966	0.82[EUR][1000 genomes]
rs4847235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847398	0.85[EUR][1000 genomes]
rs4847399	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4847401	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847402	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847408	0.82[EUR][1000 genomes]
rs4847410	0.81[EUR][1000 genomes]
rs531358	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs531514	0.82[EUR][1000 genomes]
rs535760	0.84[EUR][1000 genomes]
rs555161	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs569414	0.82[EUR][1000 genomes]
rs602204	0.84[EUR][1000 genomes]
rs612037	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61799471	0.81[ASN][1000 genomes]
rs61799496	0.80[ASN][1000 genomes]
rs624131	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs627779	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs637646	0.83[EUR][1000 genomes]
rs6541401	0.84[EUR][1000 genomes]
rs6541404	0.84[EUR][1000 genomes]
rs6680107	0.81[EUR][1000 genomes]
rs6682670	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6688230	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6703310	0.82[EUR][1000 genomes]
rs682514	0.84[EUR][1000 genomes]
rs687394	0.83[EUR][1000 genomes]
rs693737	0.84[EUR][1000 genomes]
rs7512911	0.83[EUR][1000 genomes]
rs7513705	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517363	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7524964	0.80[EUR][1000 genomes]
rs7532195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532549	0.89[EUR][1000 genomes]
rs7535628	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7537403	0.82[EUR][1000 genomes]
rs7539307	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540025	0.82[EUR][1000 genomes]
rs7541304	0.82[EUR][1000 genomes]
rs7541687	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7547244	0.82[EUR][1000 genomes]
rs7551485	0.82[EUR][1000 genomes]
rs7553465	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7553916	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs797661	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs797666	0.84[EUR][1000 genomes]
rs797671	0.81[EUR][1000 genomes]
rs797672	0.84[EUR][1000 genomes]
rs797676	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797681	0.84[EUR][1000 genomes]
rs942196	0.81[EUR][1000 genomes]
rs9432453	0.82[EUR][1000 genomes]
rs9432681	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12130734	DR1	cis	Adipose Subcutaneous	GTEx
rs12130734	RP4-717I23.3	cis	Thyroid	GTEx
rs12130734	RP4-717I23.3	cis	Artery Tibial	GTEx
rs12130734	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs12130734	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs12130734	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12130734	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12130734	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs12130734	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12130734	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs12130734	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12130734	RP4-717I23.3	cis	Whole Blood	GTEx
rs12130734	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12130734	RP4-717I23.3	cis	lung	GTEx
rs12130734	RP4-717I23.3	cis	Artery Aorta	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
2	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
4	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:93582400-93642800	Weak transcription	Gastric	stomach
6	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
8	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
9	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:93597400-93625400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
12	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
13	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:93602600-93628800	Weak transcription	Aorta	Aorta
15	chr1:93602600-93630200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:93602600-93630200	Weak transcription	Brain Anterior Caudate	brain
17	chr1:93603400-93624600	Weak transcription	Brain Substantia Nigra	brain
18	chr1:93603600-93629200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:93609000-93627400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:93611200-93626200	Strong transcription	Fetal Thymus	thymus
23	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:93613000-93626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:93613000-93626000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:93613200-93625000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:93613200-93626200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:93613200-93627800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:93613400-93625000	Strong transcription	HSMM	muscle
30	chr1:93613400-93625200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:93613600-93624600	Weak transcription	Fetal Heart	heart
32	chr1:93613600-93625600	Strong transcription	Adipose Nuclei	Adipose
33	chr1:93613600-93625800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:93613800-93625800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:93614000-93625800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:93614000-93626000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:93614000-93626200	Strong transcription	Liver	Liver
38	chr1:93614200-93625800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:93614200-93630200	Weak transcription	Right Atrium	heart
40	chr1:93614200-93634800	Weak transcription	A549	lung
41	chr1:93614400-93625800	Strong transcription	Osteobl	bone
42	chr1:93614400-93627400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:93615200-93630200	Weak transcription	Psoas Muscle	Psoas
44	chr1:93615600-93627000	Weak transcription	Ovary	ovary
45	chr1:93615600-93628400	Weak transcription	Left Ventricle	heart
46	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
47	chr1:93616000-93626400	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:93616800-93624600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:93617000-93624800	Weak transcription	K562	blood
50	chr1:93617000-93625800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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