Variant report

Variant	rs28811342
Chromosome Location	chr17:18125845-18125846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18124389..18126686-chr17:18128291..18130726,2	K562	blood:
2	chr17:18125152..18133137-chr17:18145532..18152012,9	K562	blood:
3	chr17:18055964..18057548-chr17:18123395..18125960,2	K562	blood:
4	chr17:18124758..18126506-chr17:18160763..18163317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091536	Chromatin interaction
ENSG00000131899	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10048161	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451244	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078411	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078412	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652964	0.86[EUR][1000 genomes]
rs11653988	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654146	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654177	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654741	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655588	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655731	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11655797	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656035	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11657194	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11658477	0.86[EUR][1000 genomes]
rs11868832	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868886	0.94[EUR][1000 genomes]
rs11871039	0.91[EUR][1000 genomes]
rs11871491	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600694	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563371	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563373	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16960980	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960983	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960986	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960990	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960996	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015336	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088233	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34474249	0.93[EUR][1000 genomes]
rs36058389	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55918833	0.86[EUR][1000 genomes]
rs58441148	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59354912	0.91[EUR][1000 genomes]
rs60285171	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072464	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62072465	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072466	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072467	0.94[EUR][1000 genomes]
rs62072468	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072496	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62072497	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62072498	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072500	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073602	0.85[EUR][1000 genomes]
rs62073603	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62073604	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62073605	0.89[EUR][1000 genomes]
rs62073606	0.89[EUR][1000 genomes]
rs62073607	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073608	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073609	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073611	0.90[EUR][1000 genomes]
rs62073615	0.90[EUR][1000 genomes]
rs62073649	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073650	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502640	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207276	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs735960	0.86[EUR][1000 genomes]
rs8065026	0.84[EUR][1000 genomes]
rs8069094	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077577	0.90[EUR][1000 genomes]
rs9916193	0.84[EUR][1000 genomes]
rs997315	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
14	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
15	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18112600-18127400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr17:18113000-18128200	Weak transcription	Small Intestine	intestine
3	chr17:18113200-18128200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr17:18113600-18128000	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:18113800-18127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:18113800-18127400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:18113800-18128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:18114200-18127400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr17:18114200-18127400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:18114200-18127400	Weak transcription	Left Ventricle	heart
11	chr17:18114400-18127400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:18114400-18128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:18114600-18127400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:18114600-18127800	Weak transcription	Right Ventricle	heart
15	chr17:18114600-18127800	Weak transcription	Spleen	Spleen
16	chr17:18114600-18128000	Weak transcription	Brain Germinal Matrix	brain
17	chr17:18114600-18128000	Weak transcription	Fetal Brain Female	brain
18	chr17:18114600-18128000	Weak transcription	Lung	lung
19	chr17:18114600-18128000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr17:18114600-18128200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:18114600-18128200	Weak transcription	Liver	Liver
22	chr17:18114600-18128200	Weak transcription	Brain Angular Gyrus	brain
23	chr17:18114600-18128200	Weak transcription	Brain Anterior Caudate	brain
24	chr17:18114600-18128200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr17:18114600-18128200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr17:18114600-18128200	Weak transcription	Esophagus	oesophagus
27	chr17:18114600-18128200	Weak transcription	Thymus	Thymus
28	chr17:18114600-18128200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr17:18114600-18128400	Weak transcription	Ovary	ovary
30	chr17:18114600-18128400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr17:18114800-18127400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr17:18114800-18128200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr17:18114800-18128200	Weak transcription	Fetal Thymus	thymus
34	chr17:18114800-18128400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr17:18115200-18127600	Weak transcription	Fetal Intestine Small	intestine
36	chr17:18116000-18127800	Weak transcription	Pancreas	Pancrea
37	chr17:18116200-18128200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr17:18117400-18127400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr17:18117600-18127400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:18121400-18127400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:18121400-18127400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:18121600-18128400	Weak transcription	Gastric	stomach
43	chr17:18122600-18127400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:18122600-18127400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr17:18122600-18127800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:18122600-18128200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr17:18122800-18126600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:18122800-18127400	Weak transcription	Fetal Lung	lung
49	chr17:18122800-18127400	Weak transcription	Fetal Muscle Leg	muscle
50	chr17:18122800-18127400	Weak transcription	Fetal Stomach	stomach

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