Variant report

Variant	rs9495535
Chromosome Location	chr6:139916724-139916725
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139908098..139910179-chr6:139916224..139919110,3	K562	blood:
2	chr6:139691841..139699576-chr6:139900868..139917289,34	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10223884	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12202000	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12203872	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12205687	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12211407	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1541249	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2327975	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2327976	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2876419	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4317424	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4419683	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4419684	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4557537	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4895570	0.81[AMR][1000 genomes]
rs4895574	0.81[CEU][hapmap]
rs4896478	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896479	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4896480	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4896483	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4896484	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9285491	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321734	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321735	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321737	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373239	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9376438	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9385870	0.81[CEU][hapmap]
rs9389700	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9403092	0.80[GIH][hapmap]
rs9403095	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9484293	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9484294	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9484295	0.91[ASN][1000 genomes]
rs9484298	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9495552	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9495535	REPS1	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139900800-139919200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:139907200-139919800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr6:139907600-139918400	Weak transcription	Fetal Brain Male	brain
4	chr6:139907600-139925200	Weak transcription	Aorta	Aorta
5	chr6:139908800-139920600	Enhancers	Fetal Intestine Small	intestine
6	chr6:139909400-139925200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:139909600-139918800	Weak transcription	Left Ventricle	heart
8	chr6:139909600-139923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:139910000-139918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:139910000-139918800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:139910200-139917800	Weak transcription	HMEC	breast
12	chr6:139910200-139918400	Weak transcription	Brain Germinal Matrix	brain
13	chr6:139910400-139917600	Weak transcription	NH-A	brain
14	chr6:139910600-139918400	Weak transcription	A549	lung
15	chr6:139910800-139917600	Weak transcription	Osteobl	bone
16	chr6:139910800-139918400	Weak transcription	Fetal Lung	lung
17	chr6:139911200-139918000	Weak transcription	Brain Anterior Caudate	brain
18	chr6:139913000-139917800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:139913000-139918200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:139913000-139918400	Weak transcription	Liver	Liver
21	chr6:139913000-139918800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:139913000-139928600	Weak transcription	Ovary	ovary
23	chr6:139913200-139918400	Weak transcription	HSMMtube	muscle
24	chr6:139913400-139918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:139913600-139918400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:139913600-139919200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:139913800-139917600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:139913800-139918200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:139913800-139918400	Weak transcription	Brain Angular Gyrus	brain
30	chr6:139913800-139918400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:139913800-139918600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:139913800-139918600	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:139914000-139916800	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:139914000-139917400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:139914000-139918400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:139914000-139918400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:139914200-139918600	Weak transcription	K562	blood
38	chr6:139914200-139918800	Weak transcription	Psoas Muscle	Psoas
39	chr6:139914400-139916800	Weak transcription	Pancreas	Pancrea
40	chr6:139914400-139917800	Weak transcription	Fetal Kidney	kidney
41	chr6:139914400-139925200	Weak transcription	Spleen	Spleen
42	chr6:139915000-139921000	Enhancers	Colon Smooth Muscle	Colon
43	chr6:139915600-139919200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr6:139915600-139919800	Enhancers	Stomach Mucosa	stomach
45	chr6:139915600-139920200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:139915600-139920800	Enhancers	Fetal Intestine Large	intestine
47	chr6:139915800-139917000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:139915800-139918800	Weak transcription	Esophagus	oesophagus
49	chr6:139916000-139917000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr6:139916000-139917200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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