Variant report

Variant	rs12615623
Chromosome Location	chr2:11294890-11294891
allele	A/C
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	POLR2A	chr2:11294765-11295220	A549	lung:	n/a	n/a
2	CCNT2	chr2:11294847-11295167	K562	blood:	n/a	n/a
3	POLR2A	chr2:11294711-11295310	A549	lung:	n/a	n/a
4	CBX3	chr2:11294535-11295165	K562	blood:	n/a	n/a
5	POLR2A	chr2:11294498-11295955	K562	blood:	n/a	n/a
6	ELF1	chr2:11294642-11295434	MCF-7	breast:	n/a	chr2:11295167-11295178 chr2:11295167-11295178 chr2:11295136-11295145
7	POLR2A	chr2:11294700-11295255	GM12891	blood:	n/a	n/a
8	HCFC1	chr2:11294496-11295169	K562	blood:	n/a	n/a
9	E2F6	chr2:11294713-11295237	K562	blood:	n/a	chr2:11295137-11295147
10	MAX	chr2:11294672-11296003	NB4	blood:	n/a	chr2:11294830-11294839
11	POLR2A	chr2:11294658-11295953	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIN3AK20	chr2:11294598-11296478	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr2:11294808-11295254	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr2:11294573-11295227	MCF10A-Er-Src	breast:	n/a	n/a
15	TBP	chr2:11294505-11296224	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr2:11294760-11295238	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr2:11294566-11295205	GM12891	blood:	n/a	n/a
18	SP4	chr2:11294668-11294914	H1-hESC	embryonic stem cell:	n/a	n/a
19	ELF1	chr2:11294733-11295413	GM12878	blood:	n/a	chr2:11295167-11295178 chr2:11295167-11295178 chr2:11295136-11295145
20	POLR2A	chr2:11294463-11295376	GM12878	blood:	n/a	n/a
21	MYC	chr2:11294715-11295294	K562	blood:	n/a	chr2:11294830-11294839
22	HDAC2	chr2:11294837-11295361	MCF-7	breast:	n/a	n/a
23	TAF1	chr2:11294719-11295252	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr2:11294890-11295305	K562	blood:	n/a	n/a
25	POLR2A	chr2:11294537-11295223	GM12891	blood:	n/a	n/a
26	POLR2A	chr2:11294811-11295215	A549	lung:	n/a	n/a
27	MYC	chr2:11294684-11296006	NB4	blood:	n/a	chr2:11294830-11294839
28	CTCF	chr2:11294780-11294930	GM12874	blood:	n/a	n/a
29	MAX	chr2:11294625-11296349	MCF-7	breast:	n/a	chr2:11294830-11294839
30	POLR2A	chr2:11294729-11295398	U87	brain:	n/a	n/a
31	POLR2A	chr2:11294455-11296181	GM12892	blood:	n/a	n/a
32	REST	chr2:11294837-11295242	HL-60	blood:	n/a	n/a
33	CTCF	chr2:11294740-11294890	HCFaa	heart:	n/a	n/a
34	TFAP2A	chr2:11294610-11295333	Hela-S3	cervix:	n/a	chr2:11295198-11295213 chr2:11295073-11295081 chr2:11295134-11295145 chr2:11295067-11295082 chr2:11295073-11295081 chr2:11295070-11295085 chr2:11295196-11295208 chr2:11295197-11295208 chr2:11295073-11295081
35	CTCF	chr2:11294820-11294970	GM12866	blood:	n/a	n/a
36	CTCF	chr2:11294780-11294930	HBMEC	blood vessel:	n/a	n/a
37	YY1	chr2:11294886-11295322	ECC-1	luminal epithelium:	n/a	chr2:11295133-11295147
38	TAF7	chr2:11294670-11295031	K562	blood:	n/a	n/a
39	POLR2A	chr2:11294792-11295004	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:11294811-11295958	Gliobla	brain:	n/a	n/a
41	POLR2A	chr2:11294575-11295211	H1-hESC	embryonic stem cell:	n/a	n/a
42	E2F6	chr2:11294406-11295324	A549	lung:	n/a	chr2:11294633-11294650 chr2:11295137-11295147
43	POLR2A	chr2:11294628-11295997	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr2:11294653-11296172	GM18951	blood:	n/a	n/a
45	POLR2A	chr2:11294541-11295169	PBDE	blood:	n/a	n/a
46	HEY1	chr2:11294704-11295234	K562	blood:	n/a	n/a
47	POLR2A	chr2:11294522-11295840	K562	blood:	n/a	n/a
48	POLR2A	chr2:11294826-11296049	HepG2	liver:	n/a	n/a
49	TFAP2C	chr2:11294516-11296088	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr2:11294860-11295010	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11293490..11296297-chr2:11680693..11684323,3	MCF-7	breast:
2	chr2:11273055..11275301-chr2:11293268..11296881,3	MCF-7	breast:
3	chr2:11294716..11295342-chr7:26239803..26240689,2	Hela-S3	cervix:
4	chr2:11292941..11297094-chr2:11480820..11486254,6	MCF-7	breast:
5	chr2:11273067..11276077-chr2:11294167..11297061,3	K562	blood:
6	chr2:11292794..11295094-chr2:11339407..11341727,2	MCF-7	breast:
7	chr2:11294308..11297184-chr2:11482767..11485221,3	K562	blood:
8	chr2:11271098..11275692-chr2:11293512..11297101,4	MCF-7	breast:
9	chr2:11292916..11295580-chr2:11604494..11607840,3	MCF-7	breast:
10	chr2:11284657..11286652-chr2:11293189..11295227,2	K562	blood:
11	chr2:11294400..11297941-chr2:11298345..11302243,10	MCF-7	breast:

Variant related genes	Relation type
PQLC3	TF binding region
ENSG00000162976	Chromatin interaction
ENSG00000169016	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000134318	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000150873	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10929723	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929724	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11676692	0.86[ASN][1000 genomes]
rs12612929	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617097	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12987119	0.88[ASN][1000 genomes]
rs12994920	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12995564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13000987	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13022766	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13028675	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030385	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031027	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828930	0.85[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs2037107	0.82[CEU][hapmap]
rs34315339	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34333866	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34344767	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34722769	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35536828	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36026430	0.86[ASN][1000 genomes]
rs3856468	0.91[CHB][hapmap]
rs4668714	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4669695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55691236	0.89[ASN][1000 genomes]
rs55975936	0.86[ASN][1000 genomes]
rs6744659	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6754718	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6754745	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71439048	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs727803	0.86[ASN][1000 genomes]
rs72785431	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7556705	0.81[ASN][1000 genomes]
rs7581322	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7601782	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7605804	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7606827	0.87[ASN][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	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3392188	chr2:11294026-11296874	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	esv3368553	chr2:11294376-11296624	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12615623	C2orf50	cis	parietal	SCAN
rs12615623	IAH1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11294400-11295000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
2	chr2:11294400-11295000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
3	chr2:11294400-11295000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr2:11294400-11295000	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr2:11294400-11295000	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr2:11294400-11295000	Flanking Active TSS	Hela-S3	cervix
7	chr2:11294400-11295000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr2:11294400-11295200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr2:11294400-11295200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:11294400-11295200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr2:11294400-11296000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:11294400-11296000	Active TSS	Brain Substantia Nigra	brain
13	chr2:11294600-11295000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
14	chr2:11294600-11295000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:11294600-11295000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:11294600-11295000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr2:11294600-11295000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:11294600-11295000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:11294600-11295000	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr2:11294600-11295000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:11294600-11295000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr2:11294600-11295000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr2:11294600-11295000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr2:11294600-11295000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr2:11294600-11295000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:11294600-11295000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:11294600-11295000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:11294600-11295000	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr2:11294600-11295000	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr2:11294600-11295000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:11294600-11295000	Flanking Active TSS	Colonic Mucosa	Colon
32	chr2:11294600-11295000	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr2:11294600-11295000	Flanking Active TSS	Fetal Heart	heart
34	chr2:11294600-11295000	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr2:11294600-11295000	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr2:11294600-11295000	Flanking Active TSS	Fetal Lung	lung
37	chr2:11294600-11295000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr2:11294600-11295000	Flanking Active TSS	Placenta	Placenta
39	chr2:11294600-11295000	Flanking Active TSS	Fetal Thymus	thymus
40	chr2:11294600-11295000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:11294600-11295000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr2:11294600-11295000	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr2:11294600-11295000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:11294600-11295000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr2:11294600-11295000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr2:11294600-11295000	Flanking Active TSS	Stomach Mucosa	stomach
47	chr2:11294600-11295000	Flanking Active TSS	A549	lung
48	chr2:11294600-11295000	Flanking Active TSS	GM12878-XiMat	blood
49	chr2:11294600-11295000	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr2:11294600-11295000	Flanking Active TSS	HSMM	muscle

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