Variant report

Variant	rs323893
Chromosome Location	chr3:52020411-52020412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52019831-52021815	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr3:52016371-52021465	K562	blood:	n/a	n/a
3	POLR2A	chr3:52020399-52020945	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:52018823-52021845	HepG2	liver:	n/a	n/a
5	HNF4A	chr3:52019984-52020433	HepG2	liver:	n/a	chr3:52020167-52020182
6	POLR2A	chr3:52020341-52020769	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:52019878-52020815	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52016082-52030443	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:52019747-52021787	K562	blood:	n/a	n/a
10	POLR2A	chr3:52019842-52021727	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51975678..51978117-chr3:52018353..52021936,3	MCF-7	breast:
2	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:

Variant related genes	Relation type
ABHD14B	TF binding region
ACY1	TF binding region
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566941	0.89[ASN][1000 genomes]
rs1876052	0.89[ASN][1000 genomes]
rs188953	0.81[ASW][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs2015691	0.84[YRI][hapmap]
rs2271069	0.89[ASN][1000 genomes]
rs323858	0.84[YRI][hapmap]
rs323863	0.84[YRI][hapmap]
rs323864	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs323868	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323873	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323874	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323879	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323881	1.00[ASN][1000 genomes]
rs323885	1.00[ASN][1000 genomes]
rs323886	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs323892	0.84[YRI][hapmap]
rs323894	1.00[ASN][1000 genomes]
rs323895	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323897	0.84[YRI][hapmap]
rs323898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3774344	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs379462	0.86[ASW][hapmap];0.88[YRI][hapmap]
rs380788	0.84[YRI][hapmap]
rs404527	0.84[YRI][hapmap]
rs411209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs4986825	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs56715917	0.89[ASN][1000 genomes]
rs61087263	0.89[ASN][1000 genomes]
rs6446166	0.85[ASN][1000 genomes]
rs7432986	0.80[YRI][hapmap]
rs7614743	0.89[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
11	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52017800-52020600	Enhancers	Gastric	stomach
2	chr3:52017800-52020600	Enhancers	Pancreas	Pancrea
3	chr3:52017800-52025600	Weak transcription	Ovary	ovary
4	chr3:52017800-52025600	Weak transcription	Thymus	Thymus
5	chr3:52017800-52025800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:52017800-52026000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:52017800-52026000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:52017800-52027600	Weak transcription	Fetal Brain Male	brain
9	chr3:52017800-52028200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:52017800-52028200	Weak transcription	Aorta	Aorta
11	chr3:52017800-52028600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:52018000-52022800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:52018000-52025400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:52018000-52025400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:52018000-52025400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52018000-52025600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:52018000-52025600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:52018000-52026000	Weak transcription	Primary B cells from cord blood	blood
19	chr3:52018000-52026400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:52018000-52028000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:52018200-52022400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:52018200-52023000	Weak transcription	HSMMtube	muscle
23	chr3:52018200-52023400	Weak transcription	Right Atrium	heart
24	chr3:52018200-52025400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:52018200-52025400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:52018200-52025400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:52018200-52025400	Weak transcription	Fetal Brain Female	brain
28	chr3:52018200-52025600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:52018200-52025600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr3:52018200-52025800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:52018200-52025800	Weak transcription	Primary T cells from cord blood	blood
32	chr3:52018200-52026000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:52018200-52026000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:52018200-52026200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:52018200-52026200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:52018200-52026200	Weak transcription	HUVEC	blood vessel
37	chr3:52018200-52026400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:52018200-52026600	Weak transcription	Brain Anterior Caudate	brain
39	chr3:52018200-52027400	Weak transcription	Brain Substantia Nigra	brain
40	chr3:52018200-52027600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:52018400-52022200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:52018400-52022200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:52018400-52022400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:52018400-52022400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:52018400-52022600	Weak transcription	Fetal Heart	heart
46	chr3:52018400-52023200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:52018400-52025400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:52018400-52025400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:52018400-52025400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:52018400-52025400	Weak transcription	Primary monocytes fromperipheralblood	blood

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