Variant report

Variant	rs9296193
Chromosome Location	chr6:36601456-36601457
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36600535..36602963-chr6:36638081..36640016,2	MCF-7	breast:
2	chr6:36600489..36602110-chr6:36604280..36606519,2	K562	blood:
3	chr6:36593028..36595408-chr6:36598943..36601899,2	MCF-7	breast:
4	chr6:36561858..36565797-chr6:36601247..36605469,3	K562	blood:
5	chr6:36591755..36593263-chr6:36601284..36603461,2	MCF-7	breast:
6	chr6:36598994..36606227-chr6:36643995..36648555,17	MCF-7	breast:
7	chr6:36589954..36591694-chr6:36600898..36603288,2	K562	blood:
8	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000263894	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10214849	0.83[CHD][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1061632	0.81[CEU][hapmap]
rs1076931	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10807169	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10947613	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs10947614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11755264	0.81[CEU][hapmap]
rs11756557	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11756969	0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs11757842	0.81[CEU][hapmap]
rs1191	0.81[CEU][hapmap]
rs12153820	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190062	0.81[CEU][hapmap]
rs12202732	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12208086	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12211825	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16888552	0.81[CEU][hapmap]
rs1812018	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812019	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812020	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1983781	0.81[CEU][hapmap]
rs2001101	0.94[EUR][1000 genomes]
rs2007741	0.81[CEU][hapmap]
rs2145048	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146333	0.80[CEU][hapmap]
rs2187827	0.81[CEU][hapmap]
rs2239807	0.81[CEU][hapmap]
rs2239808	0.81[CEU][hapmap]
rs2300064	0.81[CEU][hapmap]
rs3798473	0.81[CEU][hapmap]
rs3819760	0.81[CEU][hapmap]
rs4598	0.81[CEU][hapmap]
rs56144242	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61211228	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6457920	0.81[CEU][hapmap]
rs6457923	0.81[CEU][hapmap]
rs6457928	0.81[CEU][hapmap]
rs6457929	0.81[CEU][hapmap]
rs6899372	0.80[CEU][hapmap]
rs6905347	0.81[CEU][hapmap]
rs6905686	0.81[CEU][hapmap]
rs6911877	0.81[CEU][hapmap]
rs6912982	0.81[CEU][hapmap]
rs6913530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913613	0.81[CEU][hapmap]
rs6913714	0.81[CEU][hapmap]
rs6917951	0.80[CEU][hapmap]
rs6920166	0.81[CEU][hapmap]
rs6926522	0.81[CEU][hapmap]
rs6927896	0.81[CEU][hapmap]
rs6928087	0.80[CEU][hapmap]
rs6936942	0.81[CEU][hapmap]
rs6937430	0.80[EUR][1000 genomes]
rs6941593	0.81[CEU][hapmap]
rs72852338	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72852340	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741888	0.86[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7743396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7747264	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7755461	0.86[JPT][hapmap]
rs7759778	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7759933	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7760766	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7767296	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7772524	0.81[CEU][hapmap]
rs933236	0.81[CEU][hapmap]
rs9349001	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357217	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9357218	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357219	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366907	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9366908	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9366909	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368938	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368939	0.94[EUR][1000 genomes]
rs9368940	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9368943	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380577	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380578	0.82[EUR][1000 genomes]
rs9380580	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380582	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394359	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394360	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394361	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394362	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394363	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394365	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470280	0.81[CEU][hapmap]
rs9470294	0.81[CEU][hapmap]
rs9470295	0.81[CEU][hapmap]
rs9470297	0.81[CEU][hapmap]
rs9470300	0.81[CEU][hapmap]
rs9470302	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9296193	TULP1	cis	cerebellum	SCAN
rs9296193	GLO1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36581400-36604400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:36582800-36610800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:36593400-36601600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:36593600-36601800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:36595600-36601800	Weak transcription	Lung	lung
6	chr6:36595800-36601800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:36595800-36601800	Weak transcription	Fetal Thymus	thymus
8	chr6:36595800-36601800	Weak transcription	Right Ventricle	heart
9	chr6:36595800-36602000	Weak transcription	Gastric	stomach
10	chr6:36596000-36601600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:36596000-36602000	Weak transcription	HSMM	muscle
12	chr6:36597000-36603000	Enhancers	Fetal Muscle Leg	muscle
13	chr6:36597200-36601600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:36597400-36601600	Weak transcription	Right Atrium	heart
15	chr6:36597400-36601800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:36597400-36601800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:36597400-36601800	Weak transcription	Ovary	ovary
18	chr6:36597400-36602000	Weak transcription	Fetal Kidney	kidney
19	chr6:36597600-36601800	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:36598400-36601600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:36598800-36602400	Enhancers	Fetal Heart	heart
22	chr6:36599600-36601600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:36599600-36601600	Weak transcription	Left Ventricle	heart
24	chr6:36599600-36604400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:36599800-36601600	Weak transcription	Placenta	Placenta
26	chr6:36599800-36601800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:36599800-36601800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:36599800-36604600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:36599800-36604600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:36600000-36605200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:36600400-36601600	Weak transcription	Liver	Liver
32	chr6:36600400-36601600	Weak transcription	HSMMtube	muscle
33	chr6:36601000-36602400	Enhancers	Duodenum Mucosa	Duodenum
34	chr6:36601000-36602400	Enhancers	Fetal Intestine Small	intestine
35	chr6:36601000-36603400	Enhancers	Stomach Mucosa	stomach
36	chr6:36601000-36605800	Enhancers	Fetal Muscle Trunk	muscle
37	chr6:36601200-36601800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:36601200-36601800	Bivalent Enhancer	HepG2	liver
39	chr6:36601200-36602200	Enhancers	Fetal Intestine Large	intestine
40	chr6:36601200-36602400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:36601200-36602400	Enhancers	Fetal Lung	lung
42	chr6:36601200-36602400	Enhancers	Pancreas	Pancrea
43	chr6:36601200-36602400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:36601200-36602400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr6:36601200-36602400	Enhancers	HUVEC	blood vessel
46	chr6:36601200-36602400	Enhancers	NH-A	brain
47	chr6:36601200-36602600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:36601200-36603000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:36601200-36603000	Enhancers	Colonic Mucosa	Colon
50	chr6:36601200-36603200	Enhancers	Rectal Mucosa Donor 29	rectum

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