Variant report

Variant	rs880540
Chromosome Location	chr2:10914215-10914216
allele	C/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	GATA3	chr2:10913863-10914368	MCF-7	breast:	n/a	n/a
2	ESR1	chr2:10914128-10914520	T-47D	breast:	n/a	n/a
3	ESR1	chr2:10914091-10914452	T-47D	breast:	n/a	n/a
4	TCF7L2	chr2:10914200-10914872	Hela-S3	cervix:	n/a	n/a
5	MAX	chr2:10914085-10914636	MCF-7	breast:	n/a	n/a
6	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
7	NR2F2	chr2:10913703-10914580	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:10913780-10914259	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr2:10914168-10914672	Hela-S3	cervix:	n/a	n/a
10	ESR1	chr2:10914095-10914429	T-47D	breast:	n/a	n/a
11	TFAP2C	chr2:10913823-10915409	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10897607..10898216-chr2:10913767..10914408,2	MCF-7	breast:
2	chr2:10830173..10833165-chr2:10913515..10915175,3	MCF-7	breast:
3	chr2:10902594..10905238-chr2:10911928..10914865,2	MCF-7	breast:
4	chr2:10905694..10908583-chr2:10912957..10914642,3	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	chr2:10897186..10898231-chr2:10913937..10914521,3	MCF-7	breast:
10	chr2:10908984..10911442-chr2:10912799..10914956,2	MCF-7	breast:

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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]
rs1686454	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1734413	0.85[EUR][1000 genomes]
rs1734414	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2969881	0.97[EUR][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

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10903400-10914400	Weak transcription	Right Atrium	heart
2	chr2:10903600-10914400	Weak transcription	Gastric	stomach
3	chr2:10904200-10916400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:10904600-10916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:10904800-10915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:10905600-10918000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:10906200-10918200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:10906200-10918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:10908000-10918200	Weak transcription	Pancreas	Pancrea
10	chr2:10908000-10918400	Weak transcription	Aorta	Aorta
11	chr2:10908600-10924400	Weak transcription	Psoas Muscle	Psoas
12	chr2:10908800-10917400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:10908800-10918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:10909200-10914800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:10910800-10917200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:10911400-10917600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:10912200-10914400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:10912200-10916200	Enhancers	Placenta	Placenta
19	chr2:10912200-10918200	Weak transcription	Primary B cells from cord blood	blood
20	chr2:10912800-10917600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:10913000-10915400	Enhancers	Fetal Intestine Small	intestine
22	chr2:10913000-10915800	Enhancers	Fetal Muscle Trunk	muscle
23	chr2:10913000-10916000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:10913000-10916000	Enhancers	Fetal Muscle Leg	muscle
25	chr2:10913000-10916200	Enhancers	Fetal Intestine Large	intestine
26	chr2:10913200-10915600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:10913200-10917200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:10913200-10917800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:10913200-10918200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:10913200-10920200	Weak transcription	NH-A	brain
31	chr2:10913400-10914400	Enhancers	Hela-S3	cervix
32	chr2:10913400-10914600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:10913400-10915400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:10913400-10917200	Weak transcription	Thymus	Thymus
35	chr2:10913400-10920200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:10913600-10917200	Weak transcription	NHLF	lung
37	chr2:10913600-10918400	Weak transcription	HSMM	muscle
38	chr2:10913600-10919800	Weak transcription	Osteobl	bone
39	chr2:10913800-10915600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:10913800-10915600	Enhancers	HMEC	breast
41	chr2:10913800-10915800	Enhancers	Fetal Lung	lung
42	chr2:10913800-10915800	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:10913800-10916400	Enhancers	Fetal Heart	heart
44	chr2:10913800-10916600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:10913800-10917200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:10913800-10917200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:10914000-10914600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:10914000-10914600	Enhancers	HepG2	liver
49	chr2:10914000-10915000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:10914000-10915600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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