Variant report

Variant	rs7953929
Chromosome Location	chr12:123758235-123758236
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123755164..123758333-chr12:123868507..123873426,5	K562	blood:
2	chr12:123756475..123758463-chr12:123849452..123851589,2	K562	blood:
3	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
4	chr12:123755389..123758333-chr12:123866833..123870129,4	K562	blood:

Variant related genes	Relation type
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1051431	1.00[CEU][hapmap]
rs1060105	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs10732573	0.80[CEU][hapmap]
rs10772998	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10773001	0.89[EUR][1000 genomes]
rs10773002	0.81[GIH][hapmap]
rs10846486	1.00[CEU][hapmap]
rs10846491	0.92[EUR][1000 genomes]
rs11057192	0.94[CEU][hapmap]
rs11057204	0.81[EUR][1000 genomes]
rs11057206	0.81[EUR][1000 genomes]
rs11057210	0.82[EUR][1000 genomes]
rs1106240	1.00[CEU][hapmap]
rs1106241	1.00[CEU][hapmap]
rs11830103	0.84[CEU][hapmap]
rs12298826	0.94[CEU][hapmap];0.93[GIH][hapmap]
rs12304248	0.89[CEU][hapmap]
rs12316131	0.94[CEU][hapmap];0.93[GIH][hapmap]
rs12322888	0.94[CEU][hapmap];0.93[GIH][hapmap]
rs1260294	0.94[CEU][hapmap]
rs12817892	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12818067	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12824957	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12829456	0.84[EUR][1000 genomes]
rs1402274	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs1402275	0.93[GIH][hapmap];0.92[EUR][1000 genomes]
rs1533703	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs1568427	0.85[GIH][hapmap]
rs1569068	1.00[CEU][hapmap]
rs1609520	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs1615350	0.89[CEU][hapmap]
rs1617156	0.94[CEU][hapmap]
rs1716157	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs1716160	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs1716164	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs1716165	1.00[CEU][hapmap]
rs1716167	1.00[CEU][hapmap]
rs1716168	1.00[CEU][hapmap]
rs1716170	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[EUR][1000 genomes]
rs1716171	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[EUR][1000 genomes]
rs1716175	1.00[CEU][hapmap]
rs1716176	1.00[CEU][hapmap]
rs1716177	1.00[CEU][hapmap]
rs1727294	1.00[CEU][hapmap]
rs1727296	1.00[CEU][hapmap]
rs1727302	0.89[CEU][hapmap]
rs1727306	1.00[CEU][hapmap]
rs1727309	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs1727313	1.00[CEU][hapmap]
rs1727315	1.00[CEU][hapmap]
rs1727320	1.00[CEU][hapmap]
rs1727323	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs1727324	1.00[CEU][hapmap]
rs1727325	1.00[CEU][hapmap]
rs1727331	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs1727334	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs1790095	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs1790098	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs1790100	1.00[CEU][hapmap]
rs1790108	1.00[CEU][hapmap]
rs1790116	0.94[CEU][hapmap]
rs1790123	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs1790131	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs1879380	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1969354	0.94[CEU][hapmap];0.90[GIH][hapmap];0.89[EUR][1000 genomes]
rs1980252	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs2049114	1.00[CEU][hapmap]
rs2337934	0.94[CEU][hapmap];0.93[GIH][hapmap];0.91[EUR][1000 genomes]
rs2682434	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs2695478	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs2695482	1.00[CEU][hapmap]
rs28406193	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs28458312	0.94[CEU][hapmap];0.93[GIH][hapmap]
rs28472704	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs2851435	0.85[AMR][1000 genomes]
rs2851447	0.88[CEU][hapmap]
rs28569885	0.87[GIH][hapmap]
rs28625019	0.87[GIH][hapmap]
rs28636834	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs28706696	0.87[GIH][hapmap]
rs34341465	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4372492	1.00[CEU][hapmap]
rs4460848	0.89[CEU][hapmap]
rs4759371	0.94[CEU][hapmap];0.97[GIH][hapmap];0.89[EUR][1000 genomes]
rs4759409	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs4759415	0.94[CEU][hapmap];0.97[GIH][hapmap];0.91[EUR][1000 genomes]
rs4759416	0.90[EUR][1000 genomes]
rs4759417	0.91[EUR][1000 genomes]
rs4930718	0.84[GIH][hapmap]
rs58809476	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6633	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7132277	0.89[CEU][hapmap]
rs7299943	0.89[CEU][hapmap]
rs7304782	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs7306755	0.82[EUR][1000 genomes]
rs7313483	0.94[CEU][hapmap]
rs7980687	0.89[CEU][hapmap]
rs884548	1.00[CEU][hapmap]
rs941305	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs941306	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9795522	0.81[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	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
5	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7953929	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs7953929	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs7953929	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7953929	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs7953929	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs7953929	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs7953929	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123756800-123758400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123757200-123759200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:123757200-123761800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr12:123757200-123762400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:123757200-123762600	Weak transcription	GM12878-XiMat	blood
6	chr12:123757200-123773800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:123757200-123774000	Weak transcription	K562	blood
8	chr12:123757200-123782600	Weak transcription	Right Atrium	heart
9	chr12:123757400-123759200	Enhancers	Fetal Brain Male	brain
10	chr12:123757400-123762200	Weak transcription	HUVEC	blood vessel
11	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:123757600-123762000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:123757600-123762800	Weak transcription	NH-A	brain
16	chr12:123757600-123773400	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:123757600-123773400	Weak transcription	Fetal Thymus	thymus
18	chr12:123757600-123773800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:123757800-123771400	Weak transcription	A549	lung
20	chr12:123758000-123771600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:123758000-123773400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:123758200-123758400	Enhancers	Brain Germinal Matrix	brain
23	chr12:123758200-123758800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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