Variant report

Variant	rs2672571
Chromosome Location	chr12:57886609-57886610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57886183-57886649	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:57886367-57886767	K562	blood:	n/a	n/a
3	POLR2A	chr12:57886406-57886876	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:57886554-57886888	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:57886402-57886894	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:57886567-57886859	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:57886587-57886823	HepG2	liver:	n/a	n/a
8	PAX5	chr12:57886094-57886728	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:57886080-57887075	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr12:57886088-57886974	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:57886415-57886857	K562	blood:	n/a	n/a
12	POLR2A	chr12:57886413-57886711	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:57886487-57887039	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57885427..57888291-chr12:57914860..57916782,2	MCF-7	breast:
2	chr12:57879869..57888452-chr12:57905809..57918310,36	K562	blood:
3	chr12:57872773..57878513-chr12:57879040..57886839,8	K562	blood:
4	chr12:57881812..57883506-chr12:57883625..57886800,4	MCF-7	breast:
5	chr12:57632290..57634209-chr12:57884185..57886954,2	K562	blood:
6	chr12:57885435..57886938-chr12:57894343..57895911,2	MCF-7	breast:
7	chr12:57885093..57886878-chr12:57890724..57893946,3	MCF-7	breast:
8	chr12:57881044..57886958-chr12:57910925..57918058,16	MCF-7	breast:
9	chr12:57856147..57857823-chr12:57885493..57887032,2	K562	blood:
10	chr12:57879207..57888227-chr12:57906247..57918451,36	K562	blood:
11	chr12:57884095..57887084-chr12:58129295..58131672,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGAP9	TF binding region
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000264046	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1148554	0.92[CEU][hapmap]
rs1148555	0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1148557	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs1284465	0.80[AMR][1000 genomes]
rs1284605	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap]
rs1284606	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299737	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1617196	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1629410	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1669294	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1669296	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs1678537	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs1709871	0.85[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs1709874	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2127318	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs2620677	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2620679	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap]
rs2673326	0.85[AMR][1000 genomes]
rs2928382	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2943696	0.83[AMR][1000 genomes]
rs3847699	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs472895	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs474544	0.80[AMR][1000 genomes]
rs4760273	0.88[ASN][1000 genomes]
rs496245	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs508904	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs511752	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs539244	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs541869	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs542278	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs569251	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs697221	0.92[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs703835	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap]
rs703837	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs747340	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs775241	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs775324	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap]
rs776038	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs776039	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7964074	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs796546	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7969683	0.85[ASN][1000 genomes]
rs899653	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9737891	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
15	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
16	esv3364469	chr12:57886335-57888783	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
17	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2672571	ITGA7	cis	cerebellum	SCAN
rs2672571	RDH5	cis	cerebellum	SCAN
rs2672571	KRT7	cis	cerebellum	SCAN
rs2672571	DCTN2	cis	Muscle Skeletal	GTEx
rs2672571	CALCOCO1	cis	cerebellum	SCAN
rs2672571	AVIL	cis	cerebellum	SCAN
rs2672571	ACVRL1	cis	cerebellum	SCAN
rs2672571	ATF7	cis	cerebellum	SCAN
rs2672571	STAT6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57882800-57905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
3	chr12:57883200-57887000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:57883200-57887000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr12:57883200-57887000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:57883200-57887000	Strong transcription	Primary B cells from cord blood	blood
7	chr12:57883200-57887000	Strong transcription	Primary hematopoietic stem cells	blood
8	chr12:57883200-57887000	Strong transcription	Colonic Mucosa	Colon
9	chr12:57883200-57887000	Strong transcription	Fetal Intestine Large	intestine
10	chr12:57883200-57887000	Strong transcription	Fetal Lung	lung
11	chr12:57883200-57887000	Strong transcription	Placenta	Placenta
12	chr12:57883200-57890000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:57883200-57893600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:57883200-57900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:57883200-57900600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:57883200-57900800	Strong transcription	Thymus	Thymus
17	chr12:57883200-57902400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
19	chr12:57883400-57886800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:57883400-57886800	Strong transcription	Brain Angular Gyrus	brain
21	chr12:57883400-57886800	Strong transcription	Spleen	Spleen
22	chr12:57883400-57887000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:57883400-57887000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:57883400-57887000	Strong transcription	Liver	Liver
25	chr12:57883400-57887000	Strong transcription	Brain Anterior Caudate	brain
26	chr12:57883400-57887000	Strong transcription	Brain Substantia Nigra	brain
27	chr12:57883400-57887000	Strong transcription	Colon Smooth Muscle	Colon
28	chr12:57883400-57887000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:57883400-57887000	Strong transcription	Esophagus	oesophagus
30	chr12:57883400-57887000	Strong transcription	Fetal Stomach	stomach
31	chr12:57883400-57887000	Strong transcription	Left Ventricle	heart
32	chr12:57883400-57887000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:57883400-57887000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:57883400-57887000	Strong transcription	Right Ventricle	heart
35	chr12:57883400-57887000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:57883400-57887000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:57883400-57887000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:57883400-57887000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr12:57883400-57887000	Strong transcription	HUVEC	blood vessel
40	chr12:57883400-57887000	Strong transcription	NH-A	brain
41	chr12:57883400-57887000	Strong transcription	NHDF-Ad	bronchial
42	chr12:57883400-57887000	Strong transcription	NHEK	skin
43	chr12:57883400-57887000	Strong transcription	Osteobl	bone
44	chr12:57883400-57887200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:57883400-57887200	Strong transcription	Fetal Muscle Leg	muscle
46	chr12:57883400-57887400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:57883400-57887400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:57883400-57888200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:57883400-57888200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:57883400-57888200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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