Variant report

Variant	rs1879379
Chromosome Location	chr12:123727443-123727444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123721738..123724481-chr12:123725404..123728310,3	K562	blood:
2	chr12:123722318..123723838-chr12:123725541..123727819,2	MCF-7	breast:
3	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10444439	0.94[JPT][hapmap]
rs1051434	0.81[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs10732573	0.84[JPT][hapmap]
rs10744150	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10744151	0.82[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs10772997	0.81[ASN][1000 genomes]
rs10772999	0.84[ASN][1000 genomes]
rs10773000	0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10773002	0.83[ASW][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs10773003	0.94[JPT][hapmap]
rs10773005	0.94[JPT][hapmap]
rs10773921	1.00[ASW][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs10846489	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10848428	1.00[ASW][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11057202	0.81[ASN][1000 genomes]
rs11057205	0.84[ASN][1000 genomes]
rs11057207	0.84[ASN][1000 genomes]
rs11057209	0.83[ASN][1000 genomes]
rs11057219	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11057223	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11057224	0.88[ASN][1000 genomes]
rs11057251	0.90[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs11057273	0.85[JPT][hapmap]
rs11057276	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs1109559	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1109560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11608305	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs11608811	0.90[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11610710	0.80[ASN][1000 genomes]
rs12317452	0.94[JPT][hapmap]
rs12366872	0.94[JPT][hapmap]
rs1568427	0.83[ASW][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568428	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1609520	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1611973	0.82[AFR][1000 genomes]
rs1615350	0.83[ASW][hapmap]
rs1616484	0.83[AFR][1000 genomes]
rs1626703	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1716178	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1716184	0.82[AFR][1000 genomes]
rs1727286	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1727293	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727295	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1727301	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1727305	0.82[AFR][1000 genomes]
rs1727312	0.82[AFR][1000 genomes]
rs1727331	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1790088	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1790094	0.90[ASW][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1790096	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1790104	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1790106	1.00[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1790121	0.90[ASW][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1790122	0.82[AFR][1000 genomes]
rs1790129	0.84[ASN][1000 genomes]
rs1790134	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2030401	0.87[ASN][1000 genomes]
rs2271976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2280424	0.88[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2337630	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2337631	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682427	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs28410096	0.94[JPT][hapmap]
rs28532037	0.94[JPT][hapmap]
rs28533432	0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs28660993	0.94[JPT][hapmap]
rs3088303	0.94[JPT][hapmap]
rs34841857	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759114	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs4148863	0.90[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs4474478	0.83[ASN][1000 genomes]
rs4474479	0.83[ASN][1000 genomes]
rs4553407	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4594040	0.83[ASN][1000 genomes]
rs4759377	0.94[JPT][hapmap]
rs4759411	0.84[JPT][hapmap]
rs4759414	0.84[JPT][hapmap]
rs61519741	0.84[ASN][1000 genomes]
rs61953394	0.88[ASN][1000 genomes]
rs6488868	0.87[GIH][hapmap]
rs7137286	0.84[ASN][1000 genomes]
rs7139321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7304782	0.83[ASW][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7312955	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7315453	0.94[JPT][hapmap]
rs73231928	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7959415	0.84[JPT][hapmap]
rs7972811	0.94[JPT][hapmap]
rs949143	1.00[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]

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	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
2	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
3	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
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers 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
rs1879379	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1879379	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1879379	PITPNM2	cis	cerebellum	SCAN
rs1879379	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1879379	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1879379	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1879379	TMEM120B	cis	parietal	SCAN
rs1879379	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
4	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
5	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
6	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:123719200-123735200	Weak transcription	Ovary	ovary
12	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
13	chr12:123719600-123738400	Weak transcription	NH-A	brain
14	chr12:123719800-123728800	Strong transcription	Fetal Stomach	stomach
15	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
17	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
18	chr12:123720000-123732800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:123720000-123736000	Weak transcription	Gastric	stomach
20	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
21	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
22	chr12:123720600-123733000	Weak transcription	Fetal Brain Female	brain
23	chr12:123721000-123733800	Weak transcription	Lung	lung
24	chr12:123721600-123735200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:123722800-123733600	Weak transcription	Osteobl	bone
26	chr12:123723000-123733000	Weak transcription	Dnd41	blood
27	chr12:123723200-123729400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:123723200-123733000	Weak transcription	NHLF	lung
29	chr12:123723400-123735000	Weak transcription	Stomach Mucosa	stomach
30	chr12:123723600-123733000	Weak transcription	Primary B cells from cord blood	blood
31	chr12:123723800-123728200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:123724200-123727800	Strong transcription	NHEK	skin
33	chr12:123724400-123727600	Strong transcription	A549	lung
34	chr12:123724400-123733000	Weak transcription	HMEC	breast
35	chr12:123724600-123735200	Weak transcription	Placenta	Placenta
36	chr12:123725200-123738000	Weak transcription	HSMM	muscle
37	chr12:123725400-123727600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:123725800-123727600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr12:123726200-123727600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:123726200-123727600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:123726200-123727800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:123726200-123727800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:123726400-123727600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr12:123726400-123727600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:123726400-123727600	Enhancers	Adipose Nuclei	Adipose
47	chr12:123726400-123727600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr12:123726400-123727600	Enhancers	Rectal Smooth Muscle	rectum
49	chr12:123726400-123727800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:123726400-123727800	Enhancers	Colon Smooth Muscle	Colon

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