Variant report

Variant	rs323867
Chromosome Location	chr3:51977181-51977182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:157)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:157 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZEB1	chr3:51976800-51977264	GM12878	blood:	n/a	chr3:51977059-51977068
2	HCFC1	chr3:51974752-51977446	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr3:51975614-51977420	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
4	POLR2A	chr3:51975531-51977401	GM12892	blood:	n/a	n/a
5	MAZ	chr3:51975673-51977373	HepG2	liver:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
6	POLR2A	chr3:51975668-51977272	MCF10A-Er-Src	breast:	n/a	n/a
7	MAFF	chr3:51976938-51977198	HepG2	liver:	n/a	chr3:51976978-51976996
8	TBP	chr3:51976843-51977185	GM12878	blood:	n/a	n/a
9	MAX	chr3:51975393-51977389	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
10	RAD21	chr3:51975623-51977399	HCT-116	colon:	n/a	chr3:51976332-51976345 chr3:51976232-51976251 chr3:51976101-51976115 chr3:51976910-51976920
11	REST	chr3:51976881-51977257	HepG2	liver:	n/a	n/a
12	RCOR1	chr3:51977069-51977213	K562	blood:	n/a	n/a
13	TAF1	chr3:51976830-51977184	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr3:51975643-51977304	GM19099	blood:	n/a	n/a
15	MAFK	chr3:51976631-51977224	Hela-S3	cervix:	n/a	n/a
16	RFX5	chr3:51976913-51977272	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr3:51975264-51977367	Hela-S3	cervix:	n/a	n/a
18	MAZ	chr3:51975759-51977458	K562	blood:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
19	MAX	chr3:51975529-51977328	A549	lung:	n/a	chr3:51976408-51976418 chr3:51975571-51975581 chr3:51975918-51975927
20	POLR2A	chr3:51976884-51977185	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:51975679-51977274	SK-N-SH	brain:	n/a	n/a
22	EP300	chr3:51976886-51977190	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:51975538-51977688	GM12878	blood:	n/a	n/a
24	MAZ	chr3:51975699-51977270	GM12878	blood:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
25	POLR2A	chr3:51975683-51977607	Hela-S3	cervix:	n/a	n/a
26	TEAD4	chr3:51976941-51977406	HepG2	liver:	n/a	n/a
27	SMC3	chr3:51977108-51977244	HepG2	liver:	n/a	n/a
28	MYC	chr3:51975669-51977304	Hela-S3	cervix:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
29	POLR2A	chr3:51976079-51977315	PFSK-1	brain:	n/a	n/a
30	SMC3	chr3:51975711-51977506	Hela-S3	cervix:	n/a	chr3:51976533-51976540
31	MYBL2	chr3:51975777-51977214	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:51976177-51977287	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:51975667-51977266	GM18526	blood:	n/a	n/a
34	NFIC	chr3:51976901-51977248	HepG2	liver:	n/a	n/a
35	YY1	chr3:51976841-51977234	HCT-116	colon:	n/a	n/a
36	POLR2A	chr3:51975685-51977326	HepG2	liver:	n/a	n/a
37	SMARCC1	chr3:51976203-51977749	Hela-S3	cervix:	n/a	n/a
38	MXI1	chr3:51974754-51977374	IMR90	lung:	n/a	n/a
39	IRF1	chr3:51976876-51977295	K562	blood:	n/a	n/a
40	POLR2A	chr3:51975668-51977301	GM12892	blood:	n/a	n/a
41	CEBPB	chr3:51975799-51977331	Hela-S3	cervix:	n/a	n/a
42	MAX	chr3:51975687-51977190	HepG2	liver:	n/a	chr3:51976408-51976418 chr3:51975918-51975927
43	MBD4	chr3:51976922-51977392	HepG2	liver:	n/a	n/a
44	ELK1	chr3:51976996-51977212	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:51975641-51977487	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:51975669-51977271	GM19193	blood:	n/a	n/a
47	POLR2A	chr3:51976929-51977198	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr3:51976160-51977257	GM12892	blood:	n/a	n/a
49	RCOR1	chr3:51977027-51977212	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:51975676-51977487	HepG2	liver:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:73083599..73084351-chr3:51976741..51977449,2	Hela-S3	cervix:
2	chr3:51976453..51977286-chr3:142296953..142297627,2	Hela-S3	cervix:
3	chr3:51975062..51978431-chr3:52015984..52020263,5	K562	blood:
4	chr3:51974812..51978768-chr3:52006594..52010604,6	MCF-7	breast:
5	chr3:51976909..51979243-chr3:51994383..51996203,2	MCF-7	breast:
6	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
7	chr3:51974226..51977659-chr3:52020694..52024166,4	K562	blood:
8	chr3:51976676..51979243-chr3:51995471..51997610,2	K562	blood:
9	chr3:51976344..51977998-chr3:51978167..51981813,4	MCF-7	breast:
10	chr3:51974734..51977966-chr3:52006518..52010028,6	MCF-7	breast:
11	chr3:51975804..51978871-chr3:52028445..52030301,4	K562	blood:
12	chr3:51976311..51979172-chr3:51989239..51992217,2	K562	blood:
13	chr3:51974644..51978429-chr3:52029121..52032128,7	MCF-7	breast:
14	chr3:51862209..51864973-chr3:51975409..51978321,2	MCF-7	breast:
15	chr3:51975879..51978347-chr3:52015319..52018171,3	MCF-7	breast:
16	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
17	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
18	chr3:51974725..51977771-chr3:52005335..52009465,8	K562	blood:
19	chr3:51976078..51979243-chr3:51993727..51997610,4	K562	blood:
20	chr3:51976702..51977392-chr3:52029333..52029931,2	Hela-S3	cervix:
21	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
22	chr3:51976428..51980212-chr3:52001978..52006587,6	MCF-7	breast:
23	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
24	chr3:51974392..51977854-chr3:52027120..52030701,3	MCF-7	breast:
25	chr3:51739711..51741988-chr3:51976226..51978640,2	K562	blood:
26	chr3:51976380..51978109-chr3:51981388..51983019,2	MCF-7	breast:
27	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:
28	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:
29	chr3:51975678..51978117-chr3:52018353..52021936,3	MCF-7	breast:

No data

Variant related genes	Relation type
RRP9	TF binding region
PARP3	TF binding region
ENSG00000272762	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000229972	Chromatin interaction
ENSG00000164082	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000170190	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000180929	Chromatin interaction
ENSG00000248487	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

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]
rs323865	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]
rs323866	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]
rs323879	0.81[ASW][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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51975200-51977400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr3:51975600-51977200	Active TSS	HepG2	liver
3	chr3:51976200-51977200	Flanking Active TSS	Fetal Muscle Leg	muscle
4	chr3:51976200-51977200	Flanking Active TSS	Placenta	Placenta
5	chr3:51976200-51977200	Flanking Active TSS	Fetal Thymus	thymus
6	chr3:51976200-51977200	Flanking Active TSS	NH-A	brain
7	chr3:51976200-51977200	Flanking Active TSS	NHLF	lung
8	chr3:51976200-51977400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:51976200-51977400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:51976200-51977400	Flanking Active TSS	HMEC	breast
11	chr3:51976200-51977600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr3:51976200-51977600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr3:51976200-51977800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:51976400-51977200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:51976400-51977200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr3:51976400-51977200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr3:51976400-51977200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:51976400-51977200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr3:51976400-51977200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:51976400-51977200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:51976400-51977200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr3:51976400-51977200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr3:51976400-51977200	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr3:51976400-51977200	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr3:51976400-51977200	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr3:51976400-51977200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:51976400-51977200	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr3:51976400-51977200	Flanking Active TSS	Fetal Lung	lung
29	chr3:51976400-51977200	Flanking Active TSS	Fetal Stomach	stomach
30	chr3:51976400-51977200	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr3:51976400-51977200	Flanking Active TSS	Right Ventricle	heart
32	chr3:51976400-51977200	Flanking Active TSS	HUVEC	blood vessel
33	chr3:51976400-51977200	Flanking Active TSS	K562	blood
34	chr3:51976400-51977200	Flanking Active TSS	NHEK	skin
35	chr3:51976400-51977400	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr3:51976400-51977400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr3:51976400-51977400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:51976400-51977400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:51976400-51977400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:51976400-51977400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:51976400-51977400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:51976400-51977400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:51976400-51977400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:51976400-51977400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:51976400-51977400	Flanking Active TSS	Colonic Mucosa	Colon
46	chr3:51976400-51977400	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr3:51976400-51977400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:51976400-51977400	Flanking Active TSS	Dnd41	blood
49	chr3:51976400-51977400	Flanking Active TSS	HSMM	muscle
50	chr3:51976400-51977400	Flanking Active TSS	HSMMtube	muscle

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