Variant report

Variant	rs9809254
Chromosome Location	chr3:52111474-52111475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52108818..52113062-chr3:52113432..52117079,5	K562	blood:
2	chr3:52089479..52092254-chr3:52110103..52112937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs123681	0.90[EUR][1000 genomes]
rs12386365	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12496447	0.89[YRI][hapmap]
rs13314125	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs13319566	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs164638	0.88[EUR][1000 genomes]
rs164639	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17051957	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs17051977	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs171294	0.90[EUR][1000 genomes]
rs183029	0.91[EUR][1000 genomes]
rs2304505	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2334961	0.89[YRI][hapmap]
rs28452586	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28659792	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2878438	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs352146	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs352147	0.91[EUR][1000 genomes]
rs352148	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs352149	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs352150	0.91[EUR][1000 genomes]
rs352151	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs352152	0.80[YRI][hapmap]
rs352153	0.88[EUR][1000 genomes]
rs4687607	0.85[YRI][hapmap]
rs4687805	0.85[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs4687810	0.90[YRI][hapmap]
rs55664415	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55834589	0.88[EUR][1000 genomes]
rs56281986	0.87[EUR][1000 genomes]
rs56322622	0.88[EUR][1000 genomes]
rs57335685	0.91[EUR][1000 genomes]
rs57466127	0.88[EUR][1000 genomes]
rs59890038	0.91[EUR][1000 genomes]
rs6778442	0.86[YRI][hapmap]
rs6781635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72964042	0.85[EUR][1000 genomes]
rs72964044	0.91[EUR][1000 genomes]
rs731684	0.85[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs735768	0.90[YRI][hapmap]
rs747343	0.85[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs749995	0.90[YRI][hapmap]
rs7638246	0.87[EUR][1000 genomes]
rs808787	0.90[EUR][1000 genomes]
rs876782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893055	0.90[YRI][hapmap]
rs893056	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs9809977	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9811707	0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9815010	0.88[EUR][1000 genomes]
rs9816434	0.82[EUR][1000 genomes]
rs9817653	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9828327	0.93[YRI][hapmap]
rs9830293	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9841469	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9843299	0.91[EUR][1000 genomes]
rs9843852	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9846049	1.00[CEU][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9847073	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9847092	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9851576	0.86[YRI][hapmap]
rs9857878	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs9860982	0.89[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs9865330	0.83[TSI][hapmap]
rs9868101	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9882775	1.00[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
2	chr3:52102600-52121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
5	chr3:52103400-52114600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:52105600-52119600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:52105600-52120800	Strong transcription	Dnd41	blood
8	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
9	chr3:52105800-52112000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:52105800-52119200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
12	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
13	chr3:52106200-52121000	Weak transcription	HSMM	muscle
14	chr3:52106400-52112000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:52106400-52114400	Weak transcription	HMEC	breast
16	chr3:52107200-52123200	Weak transcription	Fetal Brain Female	brain
17	chr3:52107400-52113600	Strong transcription	Thymus	Thymus
18	chr3:52107600-52111600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:52108200-52114000	Weak transcription	K562	blood
20	chr3:52108400-52112800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:52108400-52113000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:52108800-52122200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:52109200-52113200	Enhancers	Fetal Muscle Leg	muscle
24	chr3:52109200-52114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:52109400-52112000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:52109400-52115000	Weak transcription	Gastric	stomach
27	chr3:52109600-52113800	Weak transcription	HepG2	liver
28	chr3:52109600-52123800	Weak transcription	NHEK	skin
29	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:52109800-52111600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:52109800-52112400	Enhancers	Brain Hippocampus Middle	brain
32	chr3:52110000-52112000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:52110000-52112000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:52110000-52112400	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:52110000-52112800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:52110000-52114800	Weak transcription	Fetal Intestine Small	intestine
37	chr3:52110000-52120000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:52110000-52121600	Weak transcription	NHLF	lung
39	chr3:52110000-52122000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:52110200-52114800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52110200-52125400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:52110400-52112200	Enhancers	Brain Substantia Nigra	brain
49	chr3:52110400-52112400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:52110400-52112400	Enhancers	Fetal Lung	lung

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