Variant report

Variant	rs323865
Chromosome Location	chr3:51975321-51975322
allele	G/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	HCFC1	chr3:51974752-51977446	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr3:51975264-51977367	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr3:51975218-51976865	SK-N-SH	brain:	n/a	chr3:51976332-51976345 chr3:51976232-51976251 chr3:51976101-51976115
4	POLR2A	chr3:51975120-51975417	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF7L2	chr3:51974744-51976522	Hela-S3	cervix:	n/a	chr3:51974830-51974839
6	POLR2A	chr3:51975318-51975330	HepG2	liver:	n/a	n/a
7	MXI1	chr3:51974754-51977374	IMR90	lung:	n/a	n/a
8	MAX	chr3:51975294-51975412	GM12878	blood:	n/a	n/a
9	WRNIP1	chr3:51975200-51975443	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:51975193-51975393	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:51975318-51977730	K562	blood:	n/a	n/a
12	MYC	chr3:51975233-51976617	A549	lung:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
13	SIN3A	chr3:51975079-51976493	H1-hESC	embryonic stem cell:	n/a	chr3:51976170-51976181
14	MXI1	chr3:51975260-51977256	GM12878	blood:	n/a	n/a
15	CEBPB	chr3:51974923-51975350	IMR90	lung:	n/a	chr3:51975090-51975101 chr3:51975089-51975100
16	SMC3	chr3:51975174-51976845	SK-N-SH	brain:	n/a	chr3:51976533-51976540
17	POLR2A	chr3:51975255-51975475	H1-hESC	embryonic stem cell:	n/a	n/a
18	RFX5	chr3:51975106-51975536	HepG2	liver:	n/a	n/a
19	SMARCB1	chr3:51975180-51977726	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr3:51974684-51977338	SK-N-SH	brain:	n/a	n/a
21	MAZ	chr3:51974972-51977431	IMR90	lung:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
22	POLR2A	chr3:51975292-51977459	K562	blood:	n/a	n/a
23	MYC	chr3:51975089-51975394	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51975062..51978431-chr3:52015984..52020263,5	K562	blood:
2	chr3:51974812..51978768-chr3:52006594..52010604,6	MCF-7	breast:
3	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
4	chr3:51974226..51977659-chr3:52020694..52024166,4	K562	blood:
5	chr3:51974734..51977966-chr3:52006518..52010028,6	MCF-7	breast:
6	chr3:51974644..51978429-chr3:52029121..52032128,7	MCF-7	breast:
7	chr3:51972961..51975805-chr3:51984917..51986970,2	MCF-7	breast:
8	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
9	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
10	chr3:51974725..51977771-chr3:52005335..52009465,8	K562	blood:
11	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
12	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
13	chr3:51974392..51977854-chr3:52027120..52030701,3	MCF-7	breast:
14	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:
15	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:

Variant related genes	Relation type
PARP3	TF binding region
ENSG00000272762	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11916396	1.00[ASN][1000 genomes]
rs188953	0.81[ASW][hapmap]
rs2015691	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323858	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323861	1.00[ASN][1000 genomes]
rs323862	1.00[ASN][1000 genomes]
rs323863	1.00[CHD][hapmap]
rs323866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323867	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323868	0.81[ASW][hapmap];0.81[AFR][1000 genomes]
rs323870	0.81[YRI][hapmap]
rs323873	0.82[LWK][hapmap]
rs323879	0.81[ASW][hapmap];0.82[LWK][hapmap];0.83[AFR][1000 genomes]
rs323886	0.81[ASW][hapmap]
rs323890	1.00[ASN][1000 genomes]
rs323892	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323897	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs379462	1.00[CHD][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs380788	1.00[ASN][1000 genomes]
rs403620	1.00[ASN][1000 genomes]
rs404527	1.00[ASN][1000 genomes]
rs433823	1.00[CHD][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs72964028	1.00[ASN][1000 genomes]
rs72964029	1.00[ASN][1000 genomes]
rs9840336	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv590280	chr3:51967439-51978327	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
8	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
9	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51973000-51975400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr3:51974200-51975400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:51974200-51975400	Flanking Active TSS	Hela-S3	cervix
4	chr3:51974200-51975600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr3:51974400-51975400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:51974400-51975400	Enhancers	Spleen	Spleen
7	chr3:51974400-51975400	Flanking Active TSS	Dnd41	blood
8	chr3:51974400-51975400	Flanking Active TSS	HSMM	muscle
9	chr3:51974400-51975600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:51974400-51975600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:51974400-51975600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:51974400-51976000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:51974400-51976400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:51974400-51976400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:51974400-51976400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:51974400-51976400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:51974600-51975400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:51974600-51975400	Flanking Active TSS	NHEK	skin
19	chr3:51974600-51975600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:51974600-51975600	Flanking Active TSS	Osteobl	bone
21	chr3:51974600-51975800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr3:51974600-51975800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr3:51974600-51976000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:51974600-51976600	Active TSS	A549	lung
25	chr3:51974600-51976800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:51974800-51975400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:51974800-51975400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:51974800-51975400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:51974800-51975400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:51974800-51975400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:51974800-51975400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:51974800-51975400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:51974800-51975400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:51974800-51975400	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr3:51974800-51975400	Flanking Active TSS	Fetal Lung	lung
36	chr3:51974800-51975400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:51974800-51975400	Flanking Active TSS	Psoas Muscle	Psoas
38	chr3:51974800-51975600	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr3:51974800-51975600	Flanking Active TSS	Fetal Brain Male	brain
40	chr3:51974800-51975600	Flanking Active TSS	Fetal Brain Female	brain
41	chr3:51974800-51975600	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr3:51974800-51975600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:51974800-51975600	Flanking Active TSS	Stomach Mucosa	stomach
44	chr3:51974800-51975800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr3:51974800-51975800	Flanking Active TSS	HUVEC	blood vessel
46	chr3:51974800-51976200	Active TSS	NHLF	lung
47	chr3:51974800-51976600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr3:51974800-51976600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:51974800-51976600	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr3:51975000-51975400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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