Variant report

Variant	rs10947639
Chromosome Location	chr6:36863834-36863835
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36853494..36856146-chr6:36862653..36865582,3	MCF-7	breast:
2	chr6:36857089..36859522-chr6:36861132..36864620,3	K562	blood:
3	chr6:36859021..36864358-chr6:36952408..36957511,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10456446	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1046578	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10498736	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947638	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947640	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10947645	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947647	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10947649	0.83[ASN][1000 genomes]
rs11757380	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11759850	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11963298	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11970506	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12110889	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12193721	0.81[EUR][1000 genomes]
rs12194154	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12202755	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12213912	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13190998	0.88[ASN][1000 genomes]
rs13199306	0.84[EUR][1000 genomes]
rs13219894	0.88[ASN][1000 genomes]
rs13219913	0.86[ASN][1000 genomes]
rs13220210	0.86[ASN][1000 genomes]
rs16889252	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272275	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2272276	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2280675	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293391	0.85[ASN][1000 genomes]
rs2293392	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395663	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3074	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34031451	0.82[ASN][1000 genomes]
rs34453243	0.81[ASN][1000 genomes]
rs34651740	0.81[ASN][1000 genomes]
rs35168332	0.84[ASN][1000 genomes]
rs35423793	0.84[ASN][1000 genomes]
rs3734331	0.80[ASN][1000 genomes]
rs3734333	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3798469	0.85[ASN][1000 genomes]
rs3957238	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4475317	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711473	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711474	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4714023	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59892114	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61006307	0.86[ASN][1000 genomes]
rs6457964	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67540019	0.87[ASN][1000 genomes]
rs6901884	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6904504	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6930737	0.81[ASN][1000 genomes]
rs6932038	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6932175	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73418143	0.86[ASN][1000 genomes]
rs7741378	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7743646	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7743836	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7757241	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7761425	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7761653	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7770155	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7774420	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296200	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9462232	0.82[ASN][1000 genomes]
rs9462233	0.93[ASN][1000 genomes]
rs9462234	0.85[ASN][1000 genomes]
rs9462235	0.83[ASN][1000 genomes]
rs9462236	0.88[ASN][1000 genomes]
rs9462238	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9462239	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9462240	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9462241	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470422	0.84[ASN][1000 genomes]
rs9470429	0.88[ASN][1000 genomes]
rs9470434	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9470439	0.83[EUR][1000 genomes]
rs9918461	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9969040	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs997674	0.82[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10947639	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854200-36868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36854200-36873600	Weak transcription	Aorta	Aorta
3	chr6:36854200-36881000	Weak transcription	Gastric	stomach
4	chr6:36854200-36887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:36854400-36868400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:36854600-36869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:36854600-36870000	Weak transcription	Stomach Mucosa	stomach
9	chr6:36854800-36866600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:36854800-36868400	Weak transcription	Brain Germinal Matrix	brain
11	chr6:36854800-36870000	Weak transcription	Colonic Mucosa	Colon
12	chr6:36854800-36875200	Weak transcription	Esophagus	oesophagus
13	chr6:36854800-36881000	Weak transcription	A549	lung
14	chr6:36854800-36882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:36854800-36884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:36855000-36866600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:36855000-36866600	Weak transcription	HUVEC	blood vessel
18	chr6:36855000-36866800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:36855000-36866800	Weak transcription	Fetal Kidney	kidney
20	chr6:36855000-36867200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:36855400-36866600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:36855400-36866600	Weak transcription	Thymus	Thymus
23	chr6:36855400-36866600	Weak transcription	NH-A	brain
24	chr6:36855400-36867200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:36855400-36868400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:36855400-36869800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:36855400-36869800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:36855400-36869800	Weak transcription	Fetal Lung	lung
29	chr6:36855400-36870000	Weak transcription	Hela-S3	cervix
30	chr6:36855400-36881000	Weak transcription	Small Intestine	intestine
31	chr6:36855600-36866200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:36855600-36866800	Weak transcription	NHLF	lung
33	chr6:36855600-36867200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:36855800-36866800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:36855800-36869800	Weak transcription	Fetal Brain Male	brain
36	chr6:36856200-36865200	Weak transcription	Fetal Brain Female	brain
37	chr6:36856200-36869800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:36856800-36869800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:36857000-36874400	Weak transcription	Pancreas	Pancrea
40	chr6:36857200-36866600	Weak transcription	HepG2	liver
41	chr6:36857200-36866800	Weak transcription	Right Ventricle	heart
42	chr6:36857200-36866800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:36857200-36870000	Weak transcription	Psoas Muscle	Psoas
44	chr6:36857400-36869800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:36858000-36866600	Weak transcription	GM12878-XiMat	blood
46	chr6:36858000-36869800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:36858200-36866800	Weak transcription	Fetal Heart	heart
48	chr6:36859600-36879400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr6:36860000-36864800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:36860200-36864000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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