Variant report

Variant	rs12213912
Chromosome Location	chr6:36860092-36860093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36853116..36855901-chr6:36858200..36860553,3	MCF-7	breast:
2	chr6:36859467..36861214-chr6:36946657..36948783,2	MCF-7	breast:
3	chr6:36841645..36844548-chr6:36858446..36860407,2	K562	blood:
4	chr6:36859021..36864358-chr6:36952408..36957511,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000137168	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1008027	0.80[JPT][hapmap]
rs1022696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10456446	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1046578	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10498736	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947638	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947639	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947640	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947645	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10947647	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947649	0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11757380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11759850	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11963298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11970506	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12110889	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12194154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12213087	0.89[GIH][hapmap]
rs13190998	0.90[ASN][1000 genomes]
rs13199306	0.86[EUR][1000 genomes]
rs13219894	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs13219913	0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13220210	0.88[ASN][1000 genomes]
rs16889252	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272275	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272276	0.95[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2280675	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2293391	0.82[ASN][1000 genomes]
rs2293392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395663	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3074	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34031451	0.84[ASN][1000 genomes]
rs34651740	0.84[ASN][1000 genomes]
rs35168332	0.86[ASN][1000 genomes]
rs35423793	0.86[ASN][1000 genomes]
rs3734333	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs3798469	0.83[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs3957238	0.90[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4475317	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711473	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711474	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4714023	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59892114	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61006307	0.88[ASN][1000 genomes]
rs6457964	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67540019	0.89[ASN][1000 genomes]
rs6901884	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904504	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6930737	0.83[ASN][1000 genomes]
rs6932038	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6932175	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs729659	0.81[ASN][1000 genomes]
rs73418143	0.88[ASN][1000 genomes]
rs7741378	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7743646	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7743836	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7757241	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7761425	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7761653	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7770155	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7774420	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296200	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462232	0.83[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9462233	0.95[ASN][1000 genomes]
rs9462234	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9462235	0.85[ASN][1000 genomes]
rs9462236	0.90[ASN][1000 genomes]
rs9462238	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462239	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9462240	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9462241	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9470422	0.83[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9470429	0.90[ASN][1000 genomes]
rs9470434	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470439	0.86[EUR][1000 genomes]
rs9918461	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9969040	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs997674	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	esv2651912	chr6:36859625-36861183	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12213912	PNPLA1	cis	parietal	SCAN
rs12213912	C6orf89	cis	parietal	SCAN
rs12213912	C6orf89	Cis_1M	lymphoblastoid	RTeQTL
rs12213912	C6orf89	cis	cerebellum	SCAN
rs12213912	LRFN2	cis	cerebellum	SCAN
rs12213912	C6orf1	cis	parietal	SCAN
rs12213912	KCNK16	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36860200	Weak transcription	Spleen	Spleen
2	chr6:36854200-36862200	Weak transcription	Lung	lung
3	chr6:36854200-36868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36854200-36873600	Weak transcription	Aorta	Aorta
5	chr6:36854200-36881000	Weak transcription	Gastric	stomach
6	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:36854400-36860200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:36854400-36868400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:36854600-36869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:36854600-36870000	Weak transcription	Stomach Mucosa	stomach
12	chr6:36854800-36861400	Weak transcription	Placenta	Placenta
13	chr6:36854800-36866600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:36854800-36868400	Weak transcription	Brain Germinal Matrix	brain
15	chr6:36854800-36870000	Weak transcription	Colonic Mucosa	Colon
16	chr6:36854800-36875200	Weak transcription	Esophagus	oesophagus
17	chr6:36854800-36881000	Weak transcription	A549	lung
18	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:36855000-36862000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr6:36855000-36862200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:36855000-36862200	Weak transcription	Fetal Intestine Large	intestine
23	chr6:36855000-36862200	Weak transcription	HMEC	breast
24	chr6:36855000-36862200	Weak transcription	HSMM	muscle
25	chr6:36855000-36862200	Weak transcription	HSMMtube	muscle
26	chr6:36855000-36866600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:36855000-36866600	Weak transcription	HUVEC	blood vessel
28	chr6:36855000-36866800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:36855000-36866800	Weak transcription	Fetal Kidney	kidney
30	chr6:36855000-36867200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:36855200-36862000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:36855200-36862200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:36855400-36861800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:36855400-36862000	Weak transcription	Adipose Nuclei	Adipose
35	chr6:36855400-36862200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:36855400-36862200	Weak transcription	Brain Substantia Nigra	brain
37	chr6:36855400-36862200	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:36855400-36862200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:36855400-36862200	Weak transcription	NHDF-Ad	bronchial
40	chr6:36855400-36866600	Weak transcription	Brain Anterior Caudate	brain
41	chr6:36855400-36866600	Weak transcription	Thymus	Thymus
42	chr6:36855400-36866600	Weak transcription	NH-A	brain
43	chr6:36855400-36867200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:36855400-36868400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:36855400-36869800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:36855400-36869800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:36855400-36869800	Weak transcription	Fetal Lung	lung
48	chr6:36855400-36870000	Weak transcription	Hela-S3	cervix
49	chr6:36855400-36881000	Weak transcription	Small Intestine	intestine
50	chr6:36855600-36862000	Weak transcription	Liver	Liver

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