Variant report

Variant	rs12139758
Chromosome Location	chr1:227260519-227260520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227258899..227260884-chr1:227261569..227263920,2	K562	blood:
2	chr1:227259571..227263475-chr1:227264453..227268699,4	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10799381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916080	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12039370	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1320494	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1483	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1929858	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2102634	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2482454	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2670462	0.80[AMR][1000 genomes]
rs2813950	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs3754418	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4351610	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs485234	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488104	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs498020	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56219094	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662583	0.83[AMR][1000 genomes]
rs6682472	0.80[AMR][1000 genomes]
rs6682642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6685823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6692080	0.80[AMR][1000 genomes]
rs6699828	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs689094	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs694740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412928	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7521110	0.83[AMR][1000 genomes]
rs7521639	0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7523167	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7543579	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7549520	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv998420	chr1:227228591-227275031	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12139758	MIXL1	cis	parietal	SCAN
rs12139758	C1orf65	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
3	chr1:227190600-227272600	Weak transcription	Lung	lung
4	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
5	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
8	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:227217000-227264400	Weak transcription	NHLF	lung
10	chr1:227217000-227271400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:227217000-227278800	Weak transcription	Placenta	Placenta
12	chr1:227220600-227272600	Weak transcription	Aorta	Aorta
13	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:227226600-227270800	Weak transcription	Fetal Brain Female	brain
15	chr1:227226800-227272400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:227226800-227278400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:227226800-227285600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:227227000-227272200	Weak transcription	Fetal Heart	heart
19	chr1:227227000-227282200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:227227400-227272400	Weak transcription	Ovary	ovary
21	chr1:227227400-227281200	Weak transcription	Fetal Kidney	kidney
22	chr1:227227400-227284200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:227228000-227277000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:227232800-227279200	Weak transcription	Stomach Mucosa	stomach
25	chr1:227235800-227271000	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:227236000-227286200	Weak transcription	Fetal Brain Male	brain
27	chr1:227238400-227270600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:227238600-227278400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:227239800-227271200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:227239800-227271400	Weak transcription	Fetal Intestine Large	intestine
31	chr1:227240000-227286800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:227240200-227266200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:227246400-227260600	Weak transcription	Osteobl	bone
34	chr1:227246400-227278400	Weak transcription	NH-A	brain
35	chr1:227247000-227260600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:227247000-227261400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227247400-227272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:227247400-227299800	Weak transcription	HMEC	breast
39	chr1:227248400-227268400	Weak transcription	Fetal Lung	lung
40	chr1:227248800-227271200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:227249400-227270400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:227249800-227271200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:227253600-227260600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:227253600-227270600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:227253600-227278600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:227253800-227261400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:227254000-227263000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:227254000-227271600	Weak transcription	Left Ventricle	heart
50	chr1:227254000-227272000	Weak transcription	Fetal Stomach	stomach

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