Variant report

Variant	rs12623872
Chromosome Location	chr2:55496078-55496079
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:403)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:403 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr2:55495915-55496593	K562	blood:	n/a	n/a
2	POLR2A	chr2:55495499-55496934	PFSK-1	brain:	n/a	n/a
3	GABPA	chr2:55495609-55496835	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:55495762-55496695	NB4	blood:	n/a	n/a
5	CEBPD	chr2:55496029-55496674	K562	blood:	n/a	n/a
6	POLR2A	chr2:55495963-55496678	MCF-7	breast:	n/a	n/a
7	ELK1	chr2:55496071-55496587	K562	blood:	n/a	n/a
8	YY1	chr2:55495932-55496730	K562	blood:	n/a	n/a
9	ELF1	chr2:55495880-55496647	MCF-7	breast:	n/a	n/a
10	NFIC	chr2:55495566-55496917	GM12878	blood:	n/a	n/a
11	MBD4	chr2:55495384-55496719	HepG2	liver:	n/a	n/a
12	PBX3	chr2:55496046-55496616	A549	lung:	n/a	n/a
13	PAX5	chr2:55495976-55496681	GM12878	blood:	n/a	chr2:55496223-55496250
14	SP4	chr2:55496049-55496583	H1-hESC	embryonic stem cell:	n/a	n/a
15	GABPA	chr2:55496021-55496757	H1-hESC	embryonic stem cell:	n/a	n/a
16	CHD1	chr2:55495812-55496751	GM12878	blood:	n/a	chr2:55496076-55496086
17	PML	chr2:55495813-55496714	K562	blood:	n/a	n/a
18	HEY1	chr2:55495577-55496683	K562	blood:	n/a	n/a
19	NR2F2	chr2:55496010-55496624	MCF-7	breast:	n/a	n/a
20	MYC	chr2:55496069-55496297	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:55496051-55496575	HepG2	liver:	n/a	n/a
22	IRF1	chr2:55495850-55497084	K562	blood:	n/a	chr2:55496048-55496057 chr2:55497054-55497064 chr2:55497052-55497063 chr2:55497053-55497065
23	SP1	chr2:55495849-55496770	A549	lung:	n/a	chr2:55496462-55496476
24	POLR2A	chr2:55495560-55496760	PANC-1	pancreas:	n/a	n/a
25	CREB1	chr2:55496078-55496717	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr2:55495893-55496628	HepG2	liver:	n/a	n/a
27	REST	chr2:55496046-55496659	PFSK-1	brain:	n/a	chr2:55496060-55496073 chr2:55496539-55496552
28	MXI1	chr2:55495646-55496655	Hela-S3	cervix:	n/a	n/a
29	TCF12	chr2:55495859-55496672	ECC-1	luminal epithelium:	n/a	n/a
30	SIN3AK20	chr2:55495532-55496909	MCF-7	breast:	n/a	n/a
31	TAF1	chr2:55495885-55496716	ECC-1	luminal epithelium:	n/a	n/a
32	STAT5A	chr2:55495992-55496759	K562	blood:	n/a	chr2:55496428-55496448
33	GABPA	chr2:55495963-55496580	Hela-S3	cervix:	n/a	n/a
34	RFX5	chr2:55496061-55496659	Hela-S3	cervix:	n/a	n/a
35	MAZ	chr2:55496035-55496704	K562	blood:	n/a	n/a
36	ETS1	chr2:55495958-55496584	K562	blood:	n/a	chr2:55496210-55496219 chr2:55496407-55496416 chr2:55496406-55496419 chr2:55496407-55496416
37	POLR2A	chr2:55495990-55496631	H1-hESC	embryonic stem cell:	n/a	n/a
38	USF1	chr2:55495629-55496655	A549	lung:	n/a	n/a
39	TAF1	chr2:55495997-55496608	H1-neurons	neurons:	n/a	n/a
40	REST	chr2:55496062-55496584	SK-N-SH	brain:	n/a	chr2:55496539-55496552
41	TEAD4	chr2:55496040-55496701	A549	lung:	n/a	n/a
42	PBX3	chr2:55495973-55496728	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr2:55495908-55496650	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr2:55496060-55496702	HepG2	liver:	n/a	n/a
45	FOXA1	chr2:55496044-55496659	HepG2	liver:	n/a	n/a
46	ATF2	chr2:55496054-55496589	H1-hESC	embryonic stem cell:	n/a	n/a
47	CREB1	chr2:55495983-55496657	GM12878	blood:	n/a	n/a
48	REST	chr2:55496010-55496592	SK-N-SH	brain:	n/a	chr2:55496060-55496073 chr2:55496539-55496552
49	NFYA	chr2:55495991-55496618	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr2:55495627-55496713	Hela-S3	cervix:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
2	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
3	chr2:55274992..55277411-chr2:55494676..55497816,3	K562	blood:
4	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
5	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
6	chr2:55496021..55497900-chr2:55843389..55845266,2	K562	blood:
7	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
8	chr2:55496021..55498315-chr2:55843389..55845953,2	K562	blood:
9	chr2:55475194..55477770-chr2:55494963..55497132,2	MCF-7	breast:
10	chr2:55495879..55496701-chr7:143598878..143599680,2	HCT-116	colon:
11	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
12	chr12:120728776..120730953-chr2:55493561..55496361,2	MCF-7	breast:
13	chr2:55494631..55497013-chr2:55842868..55845390,2	MCF-7	breast:
14	chr2:55493189..55494879-chr2:55494974..55496543,2	MCF-7	breast:
15	chr2:55274992..55276773-chr2:55494676..55496447,2	K562	blood:

No data

Variant related genes	Relation type
MTIF2	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000198420	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10188143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12619486	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs28364599	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623872	ENSG00000085760	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55494800-55497000	Active TSS	GM12878-XiMat	blood
2	chr2:55495200-55497000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:55495200-55497000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:55495200-55497200	Active TSS	Psoas Muscle	Psoas
5	chr2:55495400-55496200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr2:55495400-55496200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:55495400-55496400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:55495400-55496400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr2:55495400-55496400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr2:55495400-55496800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr2:55495400-55496800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:55495400-55496800	Active TSS	Aorta	Aorta
13	chr2:55495400-55496800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr2:55495400-55496800	Active TSS	Colonic Mucosa	Colon
15	chr2:55495400-55496800	Active TSS	Colon Smooth Muscle	Colon
16	chr2:55495400-55496800	Active TSS	Fetal Heart	heart
17	chr2:55495400-55496800	Active TSS	Left Ventricle	heart
18	chr2:55495400-55496800	Active TSS	Rectal Smooth Muscle	rectum
19	chr2:55495400-55496800	Active TSS	K562	blood
20	chr2:55495400-55496800	Active TSS	NHDF-Ad	bronchial
21	chr2:55495400-55497000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr2:55495400-55497000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr2:55495400-55497000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:55495400-55497000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:55495400-55497000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:55495400-55497000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:55495400-55497000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr2:55495400-55497000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:55495400-55497000	Active TSS	Right Atrium	heart
30	chr2:55495400-55497000	Active TSS	Right Ventricle	heart
31	chr2:55495400-55497000	Active TSS	HSMM	muscle
32	chr2:55495400-55497200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr2:55495400-55497200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:55495400-55497200	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr2:55495400-55497200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr2:55495400-55497200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:55495400-55497200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55495400-55497200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:55495400-55497200	Active TSS	Fetal Muscle Trunk	muscle
40	chr2:55495400-55497200	Active TSS	Fetal Thymus	thymus
41	chr2:55495400-55497200	Active TSS	NHLF	lung
42	chr2:55495400-55497400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55495600-55496200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr2:55495600-55496200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr2:55495600-55496200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:55495600-55496200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:55495600-55496200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr2:55495600-55496200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr2:55495600-55496400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:55495600-55496600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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