Variant report

Variant	rs1686454
Chromosome Location	chr2:10914617-10914618
allele	A/G
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	CHD2	chr2:10914601-10914842	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:10914505-10916266	SK-N-MC	brain:	n/a	n/a
3	TCF7L2	chr2:10914200-10914872	Hela-S3	cervix:	n/a	n/a
4	MAX	chr2:10914085-10914636	MCF-7	breast:	n/a	n/a
5	CEBPB	chr2:10914570-10914950	Hela-S3	cervix:	n/a	chr2:10914761-10914774
6	RCOR1	chr2:10914534-10914844	Hela-S3	cervix:	n/a	n/a
7	TFAP2A	chr2:10913830-10915380	Hela-S3	cervix:	n/a	chr2:10914839-10914847 chr2:10914699-10914714 chr2:10914206-10914216 chr2:10914839-10914847 chr2:10913942-10913953 chr2:10913942-10913953 chr2:10914361-10914373 chr2:10914204-10914218 chr2:10914839-10914847 chr2:10913942-10913953 chr2:10913937-10913952 chr2:10913942-10913953 chr2:10914206-10914216 chr2:10914206-10914216
8	MAX	chr2:10914261-10914893	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr2:10914551-10914841	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:10914510-10914622	HepG2	liver:	n/a	n/a
11	GTF2F1	chr2:10914387-10915002	Hela-S3	cervix:	n/a	n/a
12	SMC3	chr2:10914428-10914720	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr2:10914168-10914672	Hela-S3	cervix:	n/a	n/a
14	MAZ	chr2:10914590-10914822	Hela-S3	cervix:	n/a	n/a
15	TFAP2C	chr2:10913823-10915409	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10830173..10833165-chr2:10913515..10915175,3	MCF-7	breast:
2	chr2:10902594..10905238-chr2:10911928..10914865,2	MCF-7	breast:
3	chr2:10905694..10908583-chr2:10912957..10914642,3	MCF-7	breast:
4	chr2:10850840..10852513-chr2:10914222..10915993,2	MCF-7	breast:
5	chr2:10912736..10915766-chr2:10920191..10922104,3	MCF-7	breast:
6	chr2:10911679..10916866-chr2:10918103..10925152,7	K562	blood:
7	chr2:10913988..10915917-chr2:10917137..10920155,3	MCF-7	breast:
8	chr2:10913076..10914716-chr2:10924054..10926494,2	MCF-7	breast:
9	chr2:10908984..10911442-chr2:10912799..10914956,2	MCF-7	breast:

Variant related genes	Relation type
ATP6V1C2	TF binding region
ENSG00000272275	TF binding region
ENSG00000143882	Chromatin interaction
ENSG00000272275	Chromatin interaction
ENSG00000243819	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11678994	0.82[EUR][1000 genomes]
rs1387572	0.83[EUR][1000 genomes]
rs1734413	0.85[EUR][1000 genomes]
rs1734414	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2969881	0.97[EUR][1000 genomes]
rs880540	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902130	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1686454	RP11-791G15.2	cis	Esophagus Mucosa	GTEx
rs1686454	ATP6V1C2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10904200-10916400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:10904600-10916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:10904800-10915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:10905600-10918000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:10906200-10918200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:10906200-10918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:10908000-10918200	Weak transcription	Pancreas	Pancrea
8	chr2:10908000-10918400	Weak transcription	Aorta	Aorta
9	chr2:10908600-10924400	Weak transcription	Psoas Muscle	Psoas
10	chr2:10908800-10917400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:10908800-10918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:10909200-10914800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:10910800-10917200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:10911400-10917600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:10912200-10916200	Enhancers	Placenta	Placenta
16	chr2:10912200-10918200	Weak transcription	Primary B cells from cord blood	blood
17	chr2:10912800-10917600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:10913000-10915400	Enhancers	Fetal Intestine Small	intestine
19	chr2:10913000-10915800	Enhancers	Fetal Muscle Trunk	muscle
20	chr2:10913000-10916000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:10913000-10916000	Enhancers	Fetal Muscle Leg	muscle
22	chr2:10913000-10916200	Enhancers	Fetal Intestine Large	intestine
23	chr2:10913200-10915600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:10913200-10917200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:10913200-10917800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:10913200-10918200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:10913200-10920200	Weak transcription	NH-A	brain
28	chr2:10913400-10915400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:10913400-10917200	Weak transcription	Thymus	Thymus
30	chr2:10913400-10920200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:10913600-10917200	Weak transcription	NHLF	lung
32	chr2:10913600-10918400	Weak transcription	HSMM	muscle
33	chr2:10913600-10919800	Weak transcription	Osteobl	bone
34	chr2:10913800-10915600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:10913800-10915600	Enhancers	HMEC	breast
36	chr2:10913800-10915800	Enhancers	Fetal Lung	lung
37	chr2:10913800-10915800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:10913800-10916400	Enhancers	Fetal Heart	heart
39	chr2:10913800-10916600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:10913800-10917200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:10913800-10917200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:10914000-10915000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:10914000-10915600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:10914000-10915600	Enhancers	NHEK	skin
45	chr2:10914000-10916600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:10914200-10914800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:10914200-10915000	Enhancers	Lung	lung
48	chr2:10914200-10915600	Enhancers	Duodenum Mucosa	Duodenum
49	chr2:10914200-10915600	Enhancers	Left Ventricle	heart
50	chr2:10914200-10916000	Enhancers	Right Ventricle	heart

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