Variant report

Variant	rs12660989
Chromosome Location	chr6:36839054-36839055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36838369..36843263-chr6:36951921..36955568,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10947649	1.00[CEU][hapmap]
rs11542163	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751310	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751956	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753183	0.81[EUR][1000 genomes]
rs11753835	0.86[AMR][1000 genomes]
rs11757851	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11759158	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11759163	0.81[EUR][1000 genomes]
rs12660916	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191679	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192293	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200132	1.00[ASN][1000 genomes]
rs13205108	0.81[EUR][1000 genomes]
rs13205292	1.00[CEU][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]
rs13206310	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207209	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210299	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219894	0.80[CEU][hapmap]
rs13219913	0.80[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs17552005	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405617	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433592	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34597881	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869908	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913693	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35819257	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36098393	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569356	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470429	0.82[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12660989	RNF212	trans	lymphoblastoid	seeQTL
rs12660989	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36817000-36841400	Weak transcription	Colonic Mucosa	Colon
2	chr6:36817200-36841200	Weak transcription	Fetal Brain Male	brain
3	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
4	chr6:36819000-36840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:36819400-36841800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:36819800-36839800	Strong transcription	Fetal Thymus	thymus
7	chr6:36821000-36841400	Weak transcription	Small Intestine	intestine
8	chr6:36821800-36839800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:36821800-36841400	Weak transcription	HSMMtube	muscle
10	chr6:36823600-36841400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:36826200-36839800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:36826400-36841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:36826800-36840000	Strong transcription	Fetal Stomach	stomach
14	chr6:36826800-36841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:36827000-36841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:36827000-36841400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:36827000-36841400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:36827600-36839400	Strong transcription	HepG2	liver
19	chr6:36827600-36840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:36827800-36840600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:36828000-36841400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:36828200-36839800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:36828200-36841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:36828600-36841000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:36828800-36841200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:36829000-36840400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:36830000-36839400	Strong transcription	Thymus	Thymus
28	chr6:36830000-36839800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr6:36830000-36839800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:36830000-36840000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr6:36830200-36839400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr6:36830400-36839600	Strong transcription	Fetal Intestine Large	intestine
33	chr6:36830600-36840400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:36830800-36841400	Weak transcription	NHDF-Ad	bronchial
35	chr6:36831000-36839800	Strong transcription	NHEK	skin
36	chr6:36831200-36841400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:36831400-36841000	Weak transcription	NHLF	lung
38	chr6:36831800-36841400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:36831800-36841400	Weak transcription	Brain Substantia Nigra	brain
40	chr6:36831800-36841400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:36831800-36841400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:36832200-36842000	Weak transcription	Aorta	Aorta
43	chr6:36832600-36841600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:36833000-36841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:36833200-36841200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:36833200-36841400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:36833400-36840600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:36833400-36841200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:36833400-36841400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:36833400-36841400	Weak transcription	Right Atrium	heart

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