Variant report

Variant	rs715319
Chromosome Location	chr12:121287933-121287934
allele	C/T
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	CTCF	chr12:121287840-121287990	HPF	lung:	n/a	n/a
2	CTCF	chr12:121287840-121287990	SAEC	small airway:	n/a	n/a
3	BCLAF1	chr12:121287522-121288032	GM12878	blood:	n/a	n/a
4	MYC	chr12:121287723-121287972	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr12:121287840-121287990	HPAF	blood vessel:	n/a	n/a
6	FOS	chr12:121287533-121287989	MCF10A-Er-Src	breast:	n/a	chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287805-121287813 chr12:121287803-121287815
7	RUNX3	chr12:121287581-121287959	GM12878	blood:	n/a	n/a
8	FOS	chr12:121287637-121287971	MCF10A-Er-Src	breast:	n/a	chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287805-121287813 chr12:121287803-121287815
9	CTCF	chr12:121287860-121288010	HCFaa	heart:	n/a	n/a
10	CTCF	chr12:121287800-121287950	HMF	breast:	n/a	n/a
11	PBX3	chr12:121287447-121288023	SK-N-SH	brain:	n/a	chr12:121287707-121287716
12	CTCF	chr12:121287800-121287950	SAEC	small airway:	n/a	n/a
13	CTCF	chr12:121287820-121287970	NHEK	skin:	n/a	n/a
14	MYC	chr12:121287678-121287982	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr12:121287643-121287989	MCF10A-Er-Src	breast:	n/a	chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287805-121287813 chr12:121287803-121287815
16	FOS	chr12:121287620-121287984	MCF10A-Er-Src	breast:	n/a	chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287804-121287814 chr12:121287805-121287813 chr12:121287803-121287815
17	CTCF	chr12:121287820-121287970	HMEC	breast:	n/a	n/a
18	CTCF	chr12:121287820-121287970	A549	lung:	n/a	n/a
19	PBX3	chr12:121287542-121288045	SK-N-SH	brain:	n/a	chr12:121287707-121287716
20	TCF12	chr12:121287404-121288091	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr12:121287900-121288050	BJ	skin:	n/a	n/a
22	CTCF	chr12:121287860-121288010	HPAF	blood vessel:	n/a	n/a
23	IKZF1	chr12:121287526-121288007	GM12878	blood:	n/a	n/a
24	STAT3	chr12:121287545-121287940	MCF10A-Er-Src	breast:	n/a	n/a
25	CTCF	chr12:121287920-121288210	GM06990	blood:	n/a	n/a
26	CTCF	chr12:121287710-121288026	GM12878	blood:	n/a	n/a
27	ZNF143	chr12:121287750-121287942	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121280705..121284627-chr12:121285918..121289462,3	K562	blood:
2	chr12:121261119..121262624-chr12:121287692..121289232,2	MCF-7	breast:

Variant related genes	Relation type
ARF1P2	TF binding region
ENSG00000213137	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10160872	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1027556	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1039302	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10431387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10437838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10459142	0.81[ASN][1000 genomes]
rs10744754	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10774568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10774569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774570	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10774571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774573	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10774575	0.81[ASN][1000 genomes]
rs10774576	0.81[ASN][1000 genomes]
rs10849782	0.91[AMR][1000 genomes]
rs10849785	0.92[MEX][hapmap]
rs10849786	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs10849787	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10849788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10849789	0.92[MEX][hapmap]
rs10849790	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10849792	0.92[MEX][hapmap]
rs10849793	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10849794	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10849800	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849803	0.88[EUR][1000 genomes]
rs10849805	0.86[CEU][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10849806	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10849808	0.92[MEX][hapmap]
rs10849810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10849811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10849812	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10849813	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10849814	1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs11065259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11065272	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11065298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065313	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065319	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11065320	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11065321	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1151849	0.86[YRI][hapmap]
rs1151862	0.86[YRI][hapmap]
rs11829904	0.82[YRI][hapmap]
rs11833706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12310161	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12423697	0.85[EUR][1000 genomes]
rs13746	0.83[YRI][hapmap]
rs2049211	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2393718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393725	0.80[AMR][1000 genomes]
rs3213568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3213569	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap]
rs3213571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3809314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs471688	0.86[YRI][hapmap]
rs508595	0.80[YRI][hapmap]
rs531782	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs56137011	0.85[EUR][1000 genomes]
rs56161401	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs610694	0.86[YRI][hapmap]
rs624216	0.86[YRI][hapmap]
rs625228	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs6489780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6489781	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6489782	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7131886	0.86[EUR][1000 genomes]
rs7135147	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7135426	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7139145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7300695	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7315439	0.89[ASN][1000 genomes]
rs7316450	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73229114	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73229156	0.91[EUR][1000 genomes]
rs7954254	0.87[EUR][1000 genomes]
rs7960784	0.82[ASN][1000 genomes]
rs7965332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977343	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
2	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:121274400-121289400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:121274600-121289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:121274600-121289800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:121274800-121291800	Weak transcription	Dnd41	blood
7	chr12:121279200-121289200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121281600-121296200	Weak transcription	HepG2	liver
9	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
10	chr12:121282600-121288400	Enhancers	Psoas Muscle	Psoas
11	chr12:121283200-121288600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:121283200-121289200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:121283200-121291200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
15	chr12:121283400-121289400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:121283400-121289400	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:121283400-121291800	Weak transcription	Pancreas	Pancrea
18	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
19	chr12:121283600-121290800	Weak transcription	Gastric	stomach
20	chr12:121283600-121295600	Weak transcription	Fetal Stomach	stomach
21	chr12:121283600-121302200	Weak transcription	Lung	lung
22	chr12:121284000-121289200	Weak transcription	Thymus	Thymus
23	chr12:121284000-121294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:121284600-121292800	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:121285000-121289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:121285000-121290800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:121285200-121289600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:121285600-121289400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:121285600-121289400	Enhancers	A549	lung
30	chr12:121285600-121290000	Enhancers	Fetal Heart	heart
31	chr12:121285800-121289200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:121286000-121289000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:121286000-121289000	Weak transcription	Spleen	Spleen
34	chr12:121286000-121291800	Weak transcription	Fetal Intestine Small	intestine
35	chr12:121286200-121288400	Enhancers	HMEC	breast
36	chr12:121286200-121289200	Weak transcription	Brain Anterior Caudate	brain
37	chr12:121286200-121289400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:121286200-121289400	Weak transcription	Ovary	ovary
39	chr12:121286200-121289400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:121286200-121291400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:121286400-121288000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:121286400-121289000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:121286400-121289000	Enhancers	GM12878-XiMat	blood
44	chr12:121286400-121290800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:121286400-121291000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:121286400-121291000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:121286400-121291200	Weak transcription	K562	blood
48	chr12:121286400-121293800	Weak transcription	Right Ventricle	heart
49	chr12:121286600-121289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:121286600-121293600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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