Variant report

Variant	rs685384
Chromosome Location	chr6:11574362-11574363
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	chr6:11538203..11540393-chr6:11574176..11577432,3	MCF-7	breast:
2	chr6:11570134..11572268-chr6:11573159..11575300,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205269	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11751931	0.85[EUR][1000 genomes]
rs16871371	0.85[EUR][1000 genomes]
rs17607537	0.85[EUR][1000 genomes]
rs17607558	0.85[EUR][1000 genomes]
rs17675742	0.85[EUR][1000 genomes]
rs17675772	0.85[EUR][1000 genomes]
rs2140109	0.85[EUR][1000 genomes]
rs2177158	0.85[EUR][1000 genomes]
rs2177159	0.84[EUR][1000 genomes]
rs34066851	0.85[EUR][1000 genomes]
rs34255222	0.85[EUR][1000 genomes]
rs34336996	0.85[EUR][1000 genomes]
rs34342746	0.85[EUR][1000 genomes]
rs34363244	0.85[EUR][1000 genomes]
rs34486680	0.85[EUR][1000 genomes]
rs34586980	0.85[EUR][1000 genomes]
rs34630993	0.85[EUR][1000 genomes]
rs34678413	0.85[EUR][1000 genomes]
rs34793558	0.85[EUR][1000 genomes]
rs34951511	0.84[EUR][1000 genomes]
rs35074878	0.85[EUR][1000 genomes]
rs35087778	0.85[EUR][1000 genomes]
rs35100959	0.85[EUR][1000 genomes]
rs35160576	0.80[EUR][1000 genomes]
rs35250180	0.85[EUR][1000 genomes]
rs35491413	0.85[EUR][1000 genomes]
rs35658210	0.85[EUR][1000 genomes]
rs35877256	0.84[EUR][1000 genomes]
rs35938392	0.85[EUR][1000 genomes]
rs36021289	0.85[EUR][1000 genomes]
rs36023953	0.85[EUR][1000 genomes]
rs36053861	0.85[EUR][1000 genomes]
rs36120363	0.85[EUR][1000 genomes]
rs3942485	0.85[EUR][1000 genomes]
rs4711303	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs4713556	0.85[EUR][1000 genomes]
rs4713562	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs4713569	0.85[EUR][1000 genomes]
rs4713577	0.94[CEU][hapmap];0.94[JPT][hapmap]
rs4713579	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs471560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs478147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs483637	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs490466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs509971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513870	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs519140	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524159	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs528679	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs538808	0.92[ASN][1000 genomes]
rs539160	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs552681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554671	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555742	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs566237	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs571683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574254	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs581285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs586105	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs598907	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs605058	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs606402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs620729	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs62394918	0.84[EUR][1000 genomes]
rs62394920	0.85[EUR][1000 genomes]
rs62394921	0.85[EUR][1000 genomes]
rs62394922	0.85[EUR][1000 genomes]
rs62394925	0.85[EUR][1000 genomes]
rs628980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs637564	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6457608	0.85[EUR][1000 genomes]
rs661055	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663283	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66502560	0.85[EUR][1000 genomes]
rs67452935	0.85[EUR][1000 genomes]
rs675565	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67807015	0.84[EUR][1000 genomes]
rs678862	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687163	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6904209	0.83[EUR][1000 genomes]
rs6907890	0.85[EUR][1000 genomes]
rs6907900	0.85[EUR][1000 genomes]
rs6907944	0.85[EUR][1000 genomes]
rs6923613	0.85[EUR][1000 genomes]
rs6923798	0.84[EUR][1000 genomes]
rs6936326	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7752671	0.83[EUR][1000 genomes]
rs821443	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348893	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357151	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366802	0.85[EUR][1000 genomes]
rs9368729	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380321	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394108	0.85[EUR][1000 genomes]
rs9394109	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1015234	chr6:11545582-11583516	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs685384	TMEM170B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11557000-11575600	Weak transcription	Spleen	Spleen
2	chr6:11557200-11575400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:11563400-11575600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:11565200-11575400	Weak transcription	Right Ventricle	heart
5	chr6:11565800-11575400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:11567000-11579800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:11567400-11575400	Weak transcription	A549	lung
8	chr6:11567600-11575400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:11567600-11575600	Weak transcription	Brain Substantia Nigra	brain
10	chr6:11567600-11575600	Weak transcription	Left Ventricle	heart
11	chr6:11567600-11575600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:11567600-11575800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:11567600-11577400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:11567600-11581400	Weak transcription	Fetal Brain Female	brain
15	chr6:11567600-11582600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:11567600-11586200	Weak transcription	Fetal Intestine Small	intestine
17	chr6:11567600-11586400	Weak transcription	Fetal Stomach	stomach
18	chr6:11567600-11586600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:11567800-11575400	Weak transcription	Adipose Nuclei	Adipose
20	chr6:11567800-11575600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:11567800-11575600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:11567800-11575600	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:11567800-11575600	Weak transcription	HepG2	liver
24	chr6:11567800-11580000	Weak transcription	Primary B cells from cord blood	blood
25	chr6:11567800-11584200	Weak transcription	HSMMtube	muscle
26	chr6:11567800-11586400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:11568000-11577400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:11568000-11586200	Weak transcription	Liver	Liver
29	chr6:11568000-11586600	Weak transcription	Brain Angular Gyrus	brain
30	chr6:11568200-11575400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:11568200-11575800	Weak transcription	Primary T cells from cord blood	blood
32	chr6:11568200-11578200	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:11568200-11578600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:11568600-11586800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:11569400-11574800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:11570000-11575400	Weak transcription	GM12878-XiMat	blood
37	chr6:11571600-11575400	Weak transcription	Gastric	stomach
38	chr6:11571800-11575600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:11571800-11586600	Weak transcription	Ovary	ovary
40	chr6:11572400-11575800	Weak transcription	Dnd41	blood
41	chr6:11573000-11575600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:11573200-11575600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:11573400-11574400	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr6:11574000-11574800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:11574000-11575400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr6:11574000-11575600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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