Variant report

Variant	rs9828327
Chromosome Location	chr3:52120209-52120210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52118783..52120746-chr3:52151330..52153228,2	K562	blood:
2	chr3:52119415..52123026-chr3:52140546..52143765,3	K562	blood:
3	chr3:52089472..52091988-chr3:52119282..52121662,2	MCF-7	breast:
4	chr3:52117533..52120649-chr3:52132486..52135579,3	K562	blood:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12495536	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12496447	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629791	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13316105	0.81[AMR][1000 genomes]
rs2334961	1.00[CEU][hapmap];0.97[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28387060	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2878438	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs352152	0.93[CEU][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687607	0.93[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4687805	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687810	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6773704	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777340	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6778442	0.93[CEU][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786592	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs731684	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs735768	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs747343	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749995	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7616695	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7644325	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs876782	0.93[YRI][hapmap]
rs893055	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9809254	0.93[YRI][hapmap]
rs9843852	0.90[YRI][hapmap]
rs9846049	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs9851576	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9874939	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52102600-52121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
4	chr3:52105600-52120800	Strong transcription	Dnd41	blood
5	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
6	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
7	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
8	chr3:52106200-52121000	Weak transcription	HSMM	muscle
9	chr3:52107200-52123200	Weak transcription	Fetal Brain Female	brain
10	chr3:52108800-52122200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52109600-52123800	Weak transcription	NHEK	skin
12	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:52110000-52121600	Weak transcription	NHLF	lung
14	chr3:52110000-52122000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:52110200-52125400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:52110800-52122400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:52111200-52122200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52111200-52127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:52111600-52120600	Weak transcription	Lung	lung
27	chr3:52111600-52120800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:52111600-52120800	Weak transcription	Right Atrium	heart
29	chr3:52112200-52121000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:52112400-52120600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:52112400-52120600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:52112400-52122200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:52115600-52120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:52115600-52120800	Weak transcription	Fetal Intestine Large	intestine
35	chr3:52115600-52120800	Weak transcription	Fetal Stomach	stomach
36	chr3:52115800-52133000	Weak transcription	Gastric	stomach
37	chr3:52116000-52120600	Weak transcription	Placenta	Placenta
38	chr3:52117200-52120600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:52117200-52120800	Weak transcription	K562	blood
40	chr3:52117600-52120600	Weak transcription	HepG2	liver
41	chr3:52118800-52123200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52118800-52124800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:52119000-52121000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:52119000-52121200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:52119000-52123600	Enhancers	Fetal Thymus	thymus
46	chr3:52119000-52124600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:52119200-52121800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr3:52119200-52126800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:52119200-52127200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:52119200-52128400	Enhancers	Skeletal Muscle Male	skeletal muscle

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