Variant report

Variant	rs9820636
Chromosome Location	chr3:179107544-179107545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179065205..179067118-chr3:179107528..179109313,2	K562	blood:
2	chr3:179064511..179066384-chr3:179106199..179107904,2	MCF-7	breast:
3	chr3:179105113..179108152-chr3:179109096..179111055,3	K562	blood:
4	chr3:179105277..179107902-chr3:179279960..179282021,2	MCF-7	breast:
5	chr3:179105596..179108210-chr3:179108548..179111308,3	MCF-7	breast:
6	chr3:179105986..179107920-chr3:179111586..179113312,2	K562	blood:

Variant related genes	Relation type
ENSG00000136518	Chromatin interaction
ENSG00000171109	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10592	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313931	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13327891	1.00[EUR][1000 genomes]
rs28642912	1.00[EUR][1000 genomes]
rs3853150	1.00[EUR][1000 genomes]
rs3853151	1.00[EUR][1000 genomes]
rs3853152	1.00[EUR][1000 genomes]
rs6779649	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6780301	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6791769	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6795513	0.94[YRI][hapmap];0.87[AMR][1000 genomes]
rs6808409	0.94[YRI][hapmap];0.87[AMR][1000 genomes]
rs73045195	1.00[EUR][1000 genomes]
rs7355960	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7356002	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809536	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9816934	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869905	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9874433	1.00[EUR][1000 genomes]
rs9877945	0.83[YRI][hapmap]
rs9883260	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:179066800-179113600	Weak transcription	Stomach Mucosa	stomach
3	chr3:179066800-179118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:179070600-179120000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:179076400-179110600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
8	chr3:179081600-179113400	Weak transcription	Gastric	stomach
9	chr3:179081600-179115200	Weak transcription	Spleen	Spleen
10	chr3:179081600-179120400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
12	chr3:179085400-179111400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:179087200-179122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:179087600-179120000	Weak transcription	Right Ventricle	heart
15	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:179088600-179115400	Weak transcription	Aorta	Aorta
17	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
19	chr3:179098400-179120200	Weak transcription	Lung	lung
20	chr3:179098400-179125000	Weak transcription	Ovary	ovary
21	chr3:179098600-179111200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:179099000-179111600	Weak transcription	NHEK	skin
23	chr3:179099200-179111600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:179099200-179111600	Weak transcription	Esophagus	oesophagus
25	chr3:179099400-179119400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:179099600-179119600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:179099800-179113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:179101600-179125800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:179101800-179107800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:179101800-179114000	Strong transcription	Liver	Liver
31	chr3:179101800-179114200	Strong transcription	Primary B cells from cord blood	blood
32	chr3:179101800-179114400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:179101800-179115800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:179101800-179119200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:179101800-179125800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:179102000-179108800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:179102000-179109600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:179102200-179110200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:179102200-179126400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:179102400-179109800	Strong transcription	Fetal Intestine Large	intestine
42	chr3:179102400-179113800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:179103000-179112400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:179103000-179114400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:179103200-179107600	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:179103200-179108000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:179103200-179111800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:179103200-179120600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:179103400-179107800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:179103400-179108200	Strong transcription	Placenta	Placenta

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