Variant report

Variant	rs13097052
Chromosome Location	chr3:196070282-196070283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:196069769-196070402	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:196069915-196070319	MCF-7	breast:	n/a	n/a
3	NR2F2	chr3:196069826-196070425	MCF-7	breast:	n/a	n/a
4	ZNF217	chr3:196069953-196070381	MCF-7	breast:	n/a	n/a
5	HDAC2	chr3:196069837-196070404	MCF-7	breast:	n/a	n/a
6	FOXA1	chr3:196069960-196070352	T-47D	breast:	n/a	n/a
7	POLR2A	chr3:196069819-196070459	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:196069774-196070445	SK-N-MC	brain:	n/a	n/a
9	HA-E2F1	chr3:196069928-196070543	MCF-7	breast:	n/a	n/a
10	NR2F2	chr3:196069810-196070402	MCF-7	breast:	n/a	n/a
11	MYC	chr3:196070240-196070317	MCF-7	breast:	n/a	n/a
12	FOS	chr3:196070032-196070353	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr3:196070081-196070329	MCF-7	breast:	n/a	n/a
14	TCF12	chr3:196069749-196070478	MCF-7	breast:	n/a	n/a
15	GATA3	chr3:196069904-196070380	T-47D	breast:	n/a	n/a
16	GATA3	chr3:196069708-196070453	MCF-7	breast:	n/a	n/a
17	TCF12	chr3:196069736-196070421	MCF-7	breast:	n/a	n/a
18	GATA2	chr3:196070281-196070855	K562	blood:	n/a	n/a
19	TCF7L2	chr3:196069915-196070453	MCF-7	breast:	n/a	n/a
20	SIN3AK20	chr3:196069767-196070458	MCF-7	breast:	n/a	n/a
21	MAX	chr3:196069705-196070398	MCF-7	breast:	n/a	n/a
22	FOS	chr3:196070075-196070378	MCF10A-Er-Src	breast:	n/a	n/a
23	GATA3	chr3:196069957-196070476	MCF-7	breast:	n/a	n/a
24	SRF	chr3:196069830-196070370	MCF-7	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196069432..196071670-chr3:196228598..196230533,2	MCF-7	breast:
2	chr3:196040934..196046683-chr3:196067954..196076269,13	MCF-7	breast:
3	chr3:196070139..196072879-chr3:196076090..196077663,2	K562	blood:
4	chr3:196068603..196070479-chr3:196087744..196090731,2	K562	blood:
5	chr3:196068585..196071026-chr3:196125432..196127097,2	MCF-7	breast:
6	chr3:196007615..196009378-chr3:196070070..196071650,2	MCF-7	breast:
7	chr3:196069058..196070648-chr3:196099629..196101467,2	K562	blood:
8	chr3:196050354..196051997-chr3:196069518..196071791,2	MCF-7	breast:
9	chr3:196013962..196014815-chr3:196069786..196070661,4	MCF-7	breast:
10	chr3:196013398..196015851-chr3:196068583..196071493,3	MCF-7	breast:
11	chr3:196068688..196070476-chr3:196293348..196295714,2	MCF-7	breast:
12	chr3:196070078..196071619-chr3:196082742..196085208,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-910P	TF binding region
TM4SF19	TF binding region
ENSG00000161217	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000185798	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000174013	Chromatin interaction
ENSG00000243339	Chromatin interaction
ENSG00000145107	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13097255	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56152446	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
8	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
9	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
12	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
13	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
14	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
15	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
16	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
17	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
18	nsv4183	chr3:196034067-196079109	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
19	esv1836491	chr3:196051403-196078427	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13097052	RNF168	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196054600-196091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:196062800-196075000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:196065400-196071800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:196065600-196074200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:196065600-196074200	Weak transcription	HSMM	muscle
6	chr3:196065600-196075200	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:196065600-196080800	Weak transcription	HSMMtube	muscle
8	chr3:196065600-196082400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:196065600-196082600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:196065600-196084200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:196066200-196081200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:196067000-196075400	Weak transcription	Placenta	Placenta
13	chr3:196067200-196072000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:196067200-196074800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:196067400-196071400	Weak transcription	GM12878-XiMat	blood
16	chr3:196067400-196074800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:196067600-196073600	Weak transcription	A549	lung
18	chr3:196067600-196074800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:196068000-196079000	Weak transcription	Fetal Intestine Small	intestine
20	chr3:196068000-196080800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:196068400-196071400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:196068400-196072400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:196068400-196072400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:196068400-196074800	Weak transcription	Hela-S3	cervix
25	chr3:196068400-196075000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:196068400-196075200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:196068400-196075800	Weak transcription	NH-A	brain
28	chr3:196068600-196071000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:196068600-196076600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:196068600-196077600	Weak transcription	Osteobl	bone
31	chr3:196068600-196080800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:196068600-196081000	Weak transcription	NHDF-Ad	bronchial
33	chr3:196069400-196070400	Enhancers	HMEC	breast
34	chr3:196069400-196071000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:196069600-196072200	Weak transcription	Fetal Stomach	stomach
36	chr3:196069800-196070400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:196069800-196070400	Enhancers	Esophagus	oesophagus
38	chr3:196070000-196070400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:196070000-196070400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:196070000-196070400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:196070000-196070400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:196070000-196070400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:196070000-196070400	Enhancers	K562	blood
44	chr3:196070000-196070400	Flanking Active TSS	NHEK	skin
45	chr3:196070000-196070600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:196070000-196074800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:196070000-196080600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:196070200-196070400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:196070200-196070400	Enhancers	Lung	lung
50	chr3:196070200-196070800	Weak transcription	Primary monocytes fromperipheralblood	blood

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