Variant report

Variant	rs12229276
Chromosome Location	chr12:104204771-104204772
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104198690..104201561-chr12:104203107..104206456,4	K562	blood:
2	chr12:104198690..104200506-chr12:104204020..104206335,2	K562	blood:
3	chr12:104195074..104198274-chr12:104203706..104206121,4	K562	blood:
4	chr12:104199856..104205672-chr12:104232098..104237727,8	K562	blood:
5	chr12:104202983..104205031-chr12:104211895..104214839,2	K562	blood:
6	chr12:104198469..104201339-chr12:104203097..104205273,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000257754	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10861094	0.91[JPT][hapmap]
rs10861099	0.82[GIH][hapmap]
rs10861104	0.84[CEU][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10861105	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861109	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111779	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs11111781	0.82[GIH][hapmap]
rs11111782	0.82[GIH][hapmap]
rs11111783	0.82[GIH][hapmap]
rs11111786	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11111788	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11111789	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11111791	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11111792	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111793	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111796	0.95[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12228207	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12830701	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370777	0.82[GIH][hapmap]
rs1469999	0.83[YRI][hapmap]
rs1866294	0.82[GIH][hapmap]
rs1866295	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34307072	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35371470	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35746861	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35945096	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36034617	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935416	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964289	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964623	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964780	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964786	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4964794	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964805	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964806	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964812	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964814	0.82[GIH][hapmap]
rs4964820	0.82[GIH][hapmap]
rs67825151	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7134701	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs934843	0.82[GIH][hapmap]
rs934847	0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12229276	RP11-341G23.4	cis	Artery Tibial	GTEx
rs12229276	RP11-341G23.4	cis	Thyroid	GTEx
rs12229276	NEUROD6	trans	brain	seeQTL
rs12229276	C12orf45	cis	cerebellum	SCAN
rs12229276	SKA3	trans	parietal	SCAN
rs12229276	TU12B1-TY	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
6	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:104194000-104206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:104194800-104207200	Weak transcription	Adipose Nuclei	Adipose
16	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:104195000-104205200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:104195000-104207800	Weak transcription	Fetal Lung	lung
19	chr12:104195000-104208600	Weak transcription	Left Ventricle	heart
20	chr12:104195000-104213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:104195800-104208400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:104196400-104205000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:104196400-104213600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:104196400-104214800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
26	chr12:104196600-104206800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:104196600-104207800	Weak transcription	HSMMtube	muscle
28	chr12:104196600-104212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:104196600-104213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:104196800-104206400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:104196800-104206600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:104199200-104205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:104199200-104211000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:104199200-104211800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:104199600-104204800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:104199600-104205000	Genic enhancers	Colon Smooth Muscle	Colon
37	chr12:104199600-104214600	Weak transcription	Esophagus	oesophagus
38	chr12:104200000-104214600	Weak transcription	Ovary	ovary
39	chr12:104200200-104204800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:104200200-104207000	Weak transcription	Liver	Liver
41	chr12:104200200-104216200	Weak transcription	NHDF-Ad	bronchial
42	chr12:104200400-104210000	Weak transcription	Hela-S3	cervix
43	chr12:104200800-104205600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:104200800-104207200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:104201000-104205200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:104201000-104205200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:104201000-104205400	Weak transcription	HepG2	liver
48	chr12:104201000-104206600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:104201000-104214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:104201200-104205200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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