Variant report

Variant	rs2030401
Chromosome Location	chr12:123751339-123751340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123460655..123463100-chr12:123749736..123752602,2	MCF-7	breast:
2	chr12:123717082..123719698-chr12:123751267..123753093,2	K562	blood:
3	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:
4	chr12:123749665..123751681-chr12:124116625..124119376,2	MCF-7	breast:
5	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10732573	0.82[ASN][1000 genomes]
rs10734901	0.82[ASN][1000 genomes]
rs10773000	0.91[ASN][1000 genomes]
rs10846489	0.98[ASN][1000 genomes]
rs11057219	0.98[ASN][1000 genomes]
rs11057223	0.94[ASN][1000 genomes]
rs11057224	0.99[ASN][1000 genomes]
rs1109559	0.97[ASN][1000 genomes]
rs1109560	0.98[ASN][1000 genomes]
rs1568428	0.89[ASN][1000 genomes]
rs1879379	0.87[ASN][1000 genomes]
rs1969355	0.80[ASN][1000 genomes]
rs1980251	0.82[ASN][1000 genomes]
rs2271976	0.99[ASN][1000 genomes]
rs2337630	0.88[ASN][1000 genomes]
rs2337631	0.88[ASN][1000 genomes]
rs34841857	0.87[ASN][1000 genomes]
rs3759114	0.81[ASN][1000 genomes]
rs4553407	0.99[ASN][1000 genomes]
rs4759372	0.80[ASN][1000 genomes]
rs4759413	0.82[ASN][1000 genomes]
rs4759414	0.82[ASN][1000 genomes]
rs61953394	0.99[ASN][1000 genomes]
rs7139321	0.84[ASN][1000 genomes]
rs7312955	0.89[ASN][1000 genomes]
rs73231928	0.84[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2030401	MGC7036	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
3	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
4	chr12:123736000-123752200	Strong transcription	Dnd41	blood
5	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:123736400-123752600	Strong transcription	NHLF	lung
8	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
9	chr12:123737200-123752000	Strong transcription	A549	lung
10	chr12:123738000-123751800	Strong transcription	Liver	Liver
11	chr12:123738000-123751800	Strong transcription	Fetal Intestine Large	intestine
12	chr12:123738000-123752000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr12:123738000-123752000	Strong transcription	HUVEC	blood vessel
14	chr12:123738000-123752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:123738000-123752800	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr12:123738200-123751800	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:123738200-123752000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:123738600-123752200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:123739000-123751600	Strong transcription	Placenta	Placenta
20	chr12:123739200-123751800	Strong transcription	Adipose Nuclei	Adipose
21	chr12:123739200-123752600	Weak transcription	Psoas Muscle	Psoas
22	chr12:123739200-123753000	Weak transcription	Right Atrium	heart
23	chr12:123739200-123753200	Weak transcription	Fetal Heart	heart
24	chr12:123739200-123754200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:123739400-123751800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:123739800-123751400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:123739800-123752400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:123739800-123753200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:123740000-123753600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:123741000-123752200	Strong transcription	Osteobl	bone
31	chr12:123741000-123753600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:123742000-123752600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:123742400-123753400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:123742400-123754600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:123742400-123754600	Weak transcription	Small Intestine	intestine
36	chr12:123743000-123754200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:123743200-123751800	Strong transcription	Aorta	Aorta
38	chr12:123743400-123751800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:123743400-123752400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:123743400-123754000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:123743600-123752200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:123743600-123753600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:123743800-123752000	Strong transcription	Fetal Thymus	thymus
44	chr12:123743800-123752200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:123743800-123752600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:123743800-123752600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:123744000-123752400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:123744000-123753800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:123744000-123753800	Weak transcription	K562	blood
50	chr12:123744600-123752600	Weak transcription	Primary B cells from cord blood	blood

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