Variant report

Variant	rs12898604
Chromosome Location	chr15:60648214-60648215
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:5)
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	POLR2A	chr15:60647340-60648598	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr15:60646747-60648614	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr15:60642299-60649868	U87	brain:	n/a	n/a
4	POLR2A	chr15:60632288-60649793	U87	brain:	n/a	n/a
5	POLR2A	chr15:60648199-60648337	A549	lung:	n/a	n/a
6	POLR2A	chr15:60646807-60648368	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr15:60647198-60648365	ProgFib	skin:	n/a	n/a
8	POLR2A	chr15:60640890-60648672	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr15:60646890-60648747	U87	brain:	n/a	n/a
10	POLR2A	chr15:60647988-60648248	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr15:60646990-60648419	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr15:60648092-60648559	HCT-116	colon:	n/a	n/a
13	POLR2A	chr15:60646890-60649648	U87	brain:	n/a	n/a
14	POLR2A	chr15:60646843-60648819	HUVEC	blood vessel:	n/a	n/a
15	NFYB	chr15:60648057-60648257	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:60646899-60648765	K562	blood:	n/a	n/a
17	POLR2A	chr15:60648174-60648538	HUVEC	blood vessel:	n/a	n/a
18	JUND	chr15:60646980-60648385	A549	lung:	n/a	n/a
19	POLR2A	chr15:60646864-60648611	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:60648131-60648589	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:60646735-60649728	A549	lung:	n/a	n/a
22	POLR2A	chr15:60646730-60648785	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr15:60646250-60648657	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr15:60640865-60648721	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:60647549..60649516-chr15:60685389..60686979,2	MCF-7	breast:
2	chr15:60643760..60646318-chr15:60647348..60649843,3	K562	blood:
3	chr15:60645904..60648374-chr15:60685084..60687968,2	K562	blood:
4	chr15:60647640..60653087-chr15:60688759..60691610,5	K562	blood:
5	chr15:60646064..60648363-chr15:60769795..60771520,2	K562	blood:

No data

Variant related genes	Relation type
ANXA2	TF binding region
ENSG00000128915	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000182718	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1033027	0.88[EUR][1000 genomes]
rs10851676	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10851678	0.83[ASN][1000 genomes]
rs10851679	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071519	0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11071521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap]
rs11631793	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631850	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634259	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854079	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439973	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12440492	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708462	0.83[EUR][1000 genomes]
rs12899562	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs12904910	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551349	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1567408	0.87[EUR][1000 genomes]
rs1967370	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014953	0.87[EUR][1000 genomes]
rs2063322	0.87[EUR][1000 genomes]
rs2063324	0.87[EUR][1000 genomes]
rs2063325	0.86[EUR][1000 genomes]
rs2085037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2123828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2123833	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2136553	0.88[EUR][1000 genomes]
rs2136555	0.87[EUR][1000 genomes]
rs2168013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175187	0.88[EUR][1000 genomes]
rs2202920	0.87[EUR][1000 genomes]
rs2414667	0.88[EUR][1000 genomes]
rs2414668	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414670	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3743269	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743270	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825957	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4485290	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4530072	0.85[ASN][1000 genomes]
rs4775257	0.86[EUR][1000 genomes]
rs7165592	0.88[EUR][1000 genomes]
rs7167571	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7170178	0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7170421	0.86[ASN][1000 genomes]
rs7172784	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178033	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7179548	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7180174	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027359	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8029375	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033896	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8037326	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039867	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9920432	0.81[EUR][1000 genomes]
rs9920513	0.82[ASN][1000 genomes]
rs9920684	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9920883	0.87[EUR][1000 genomes]
rs9972449	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12898604	C2CD4A	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60633000-60651400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:60634600-60651200	Genic enhancers	A549	lung
3	chr15:60635600-60650000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:60636000-60651800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:60636400-60648600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:60636600-60657800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:60637000-60654800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:60637200-60649600	Strong transcription	Esophagus	oesophagus
9	chr15:60637200-60649800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:60637200-60652800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:60637200-60653600	Strong transcription	Placenta	Placenta
12	chr15:60637200-60654000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr15:60637200-60656800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:60637200-60656800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:60637400-60649600	Strong transcription	Colonic Mucosa	Colon
16	chr15:60637400-60658000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:60637600-60650200	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:60637600-60651400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:60637600-60658000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:60637800-60649400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:60637800-60649400	Strong transcription	Ovary	ovary
22	chr15:60637800-60649600	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:60637800-60650000	Strong transcription	Fetal Intestine Small	intestine
24	chr15:60637800-60652400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:60638000-60654200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:60638000-60654600	Strong transcription	NHEK	skin
27	chr15:60638000-60655000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:60638200-60649600	Strong transcription	Colon Smooth Muscle	Colon
29	chr15:60638200-60649600	Strong transcription	Fetal Lung	lung
30	chr15:60638200-60650800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:60638200-60655000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:60638400-60649200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr15:60638400-60651800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:60638400-60656800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:60638600-60648400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:60638600-60649800	Strong transcription	GM12878-XiMat	blood
37	chr15:60639000-60649600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:60639600-60656800	Strong transcription	HepG2	liver
39	chr15:60640000-60657800	Strong transcription	Fetal Intestine Large	intestine
40	chr15:60640200-60650000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr15:60640200-60650200	Strong transcription	Lung	lung
42	chr15:60640600-60650000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:60640600-60656200	Weak transcription	Fetal Thymus	thymus
44	chr15:60640600-60656800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:60640600-60657200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:60640600-60657800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:60641600-60658000	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr15:60641800-60649800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:60642200-60649600	Strong transcription	Pancreas	Pancrea
50	chr15:60642400-60649400	Strong transcription	Primary T cells from cord blood	blood

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