Variant report

Variant	rs323871
Chromosome Location	chr3:51990605-51990606
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51989698..51992601-chr3:51995625..51997375,2	MCF-7	breast:
2	chr3:51985563..51987517-chr3:51990241..51992502,2	MCF-7	breast:
3	chr3:51987928..51991924-chr3:52001407..52003695,4	MCF-7	breast:
4	chr3:51988009..51992311-chr3:51992660..51997455,6	K562	blood:
5	chr3:51976311..51979172-chr3:51989239..51992217,2	K562	blood:
6	chr3:51988573..51991523-chr3:52028412..52030001,2	K562	blood:
7	chr3:51985305..51989166-chr3:51989564..51992012,3	K562	blood:

Variant related genes	Relation type
ENSG00000041880	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1566941	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1876052	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188953	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2015691	0.90[AMR][1000 genomes]
rs2271069	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323864	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs323868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323881	1.00[ASN][1000 genomes]
rs323885	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323897	0.90[AMR][1000 genomes]
rs323898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs379462	0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs380788	0.90[AMR][1000 genomes]
rs404527	0.90[AMR][1000 genomes]
rs411209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs4986825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56715917	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61087263	0.89[ASN][1000 genomes]
rs6446166	0.85[ASN][1000 genomes]
rs72964028	0.90[AMR][1000 genomes]
rs72964029	0.80[AMR][1000 genomes]
rs7614743	0.89[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

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	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	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh 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	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
6	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
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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
8	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
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	esv3438711	chr3:51987612-51992410	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv3405551	chr3:51989162-51991160	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
2	chr3:51986200-51993400	Weak transcription	HepG2	liver
3	chr3:51987600-51992000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:51988000-51990800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:51988000-51990800	Weak transcription	HSMM	muscle
6	chr3:51988000-51992400	Weak transcription	HSMMtube	muscle
7	chr3:51988400-52000600	Weak transcription	Hela-S3	cervix
8	chr3:51989200-51990800	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr3:51989200-51991000	Enhancers	Fetal Brain Male	brain
10	chr3:51989200-51991000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr3:51989200-51991200	Enhancers	Spleen	Spleen
12	chr3:51989200-51991400	Enhancers	Liver	Liver
13	chr3:51989200-51991400	Enhancers	Fetal Heart	heart
14	chr3:51989400-51990800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:51989400-51991000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:51989400-51991800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:51989400-51997000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:51989600-51990800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:51989600-51990800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr3:51989600-51990800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:51989600-51990800	Active TSS	Brain Anterior Caudate	brain
22	chr3:51989600-51990800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
23	chr3:51989600-51990800	Flanking Active TSS	Right Ventricle	heart
24	chr3:51989800-51990800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:51989800-51990800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:51989800-51990800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:51989800-51990800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr3:51989800-51990800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:51989800-51990800	Active TSS	Fetal Brain Female	brain
30	chr3:51989800-51990800	Flanking Active TSS	Pancreas	Pancrea
31	chr3:51989800-51990800	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr3:51989800-51990800	Flanking Bivalent TSS/Enh	Thymus	Thymus
33	chr3:51989800-51991000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:51989800-51991000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr3:51989800-51991200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr3:51990000-51990800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:51990000-51990800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr3:51990000-51990800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:51990000-51990800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr3:51990000-51991000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
41	chr3:51990000-51991000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:51990200-51990800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr3:51990200-51990800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr3:51990200-51990800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
45	chr3:51990200-51990800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:51990200-51990800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:51990200-51991000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:51990200-51991000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:51990200-51991800	Weak transcription	Lung	lung
50	chr3:51990400-51990800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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