Variant report

Variant	rs9375554
Chromosome Location	chr6:128547549-128547550
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10485160	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11961542	0.84[ASN][1000 genomes]
rs12055654	0.85[ASN][1000 genomes]
rs12055776	0.82[CHB][hapmap];0.87[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543376	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs17055441	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17055450	1.00[YRI][hapmap]
rs17055452	1.00[YRI][hapmap]
rs17055472	0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs17055477	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2073161	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076572	0.84[ASN][1000 genomes]
rs4140541	0.88[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4140542	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243494	1.00[MEX][hapmap]
rs4483000	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4628122	1.00[TSI][hapmap]
rs61422755	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61583694	0.84[ASN][1000 genomes]
rs6928143	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs6930547	0.91[ASN][1000 genomes]
rs730202	0.81[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs73590673	0.85[ASN][1000 genomes]
rs742736	0.88[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs7755473	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755836	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7773849	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9321113	0.88[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9372886	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9372887	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375552	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9375553	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs9375555	0.88[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs9375556	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375557	0.85[ASN][1000 genomes]
rs9375558	0.84[ASN][1000 genomes]
rs9385452	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385454	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385455	0.83[ASN][1000 genomes]
rs9388623	0.90[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs9388624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388625	0.85[ASN][1000 genomes]
rs9388626	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9388627	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9388629	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs9398864	0.91[ASN][1000 genomes]
rs9398865	0.87[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs9398867	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398868	0.88[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs9402023	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9402024	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9402025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9402027	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402029	0.83[ASN][1000 genomes]
rs9402030	0.88[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs9402031	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402032	0.83[CHB][hapmap]
rs9784773	0.88[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9784880	0.88[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv886653	chr6:128455539-128555805	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv886654	chr6:128471938-128555805	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128505800-128552200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
8	chr6:128528200-128558400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
10	chr6:128529400-128552600	Weak transcription	Small Intestine	intestine
11	chr6:128529800-128561000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:128531000-128550600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
14	chr6:128531200-128554600	Weak transcription	Right Ventricle	heart
15	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
16	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:128531400-128553600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:128532000-128554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:128532000-128561000	Weak transcription	Osteobl	bone
21	chr6:128532200-128553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:128536000-128554800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:128536800-128560600	Weak transcription	Fetal Lung	lung
24	chr6:128537200-128561000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:128539800-128552400	Weak transcription	Liver	Liver
27	chr6:128539800-128558200	Weak transcription	NH-A	brain
28	chr6:128540200-128552800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:128540200-128556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:128540200-128559600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:128540200-128561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:128540400-128551200	Weak transcription	HSMM	muscle
34	chr6:128540400-128554400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:128540400-128560400	Weak transcription	Fetal Thymus	thymus
36	chr6:128540400-128560400	Weak transcription	HUVEC	blood vessel
37	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:128540600-128550200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:128540600-128561000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:128540800-128562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:128541000-128551200	Weak transcription	Primary B cells from cord blood	blood
42	chr6:128542400-128551000	Weak transcription	HepG2	liver
43	chr6:128543800-128550200	Weak transcription	Stomach Mucosa	stomach
44	chr6:128544000-128556600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:128544200-128550000	Weak transcription	Fetal Intestine Small	intestine
46	chr6:128544200-128562400	Weak transcription	Gastric	stomach
47	chr6:128544200-128563200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:128547000-128548400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:128547000-128548600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:128547000-128548600	Enhancers	NHEK	skin

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