Variant report

Variant	rs1388597
Chromosome Location	chr12:40618097-40618098
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	MAZ	chr12:40617778-40619458	IMR90	lung:	n/a	chr12:40618784-40618793
2	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
3	POLR2A	chr12:40617796-40619536	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF263	chr12:40617969-40619401	HEK293-T-REx	kidney:	n/a	chr12:40618700-40618709 chr12:40619158-40619167 chr12:40618762-40618771
5	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
6	RELA	chr12:40617863-40619486	GM18951	blood:	n/a	n/a
7	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
8	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
9	TCF12	chr12:40617809-40619771	A549	lung:	n/a	chr12:40618605-40618615
10	REST	chr12:40618023-40619814	A549	lung:	n/a	chr12:40618846-40618856 chr12:40618853-40618866 chr12:40618751-40618761
11	GATA2	chr12:40617993-40619425	SH-SY5Y	brain:	n/a	chr12:40618106-40618116
12	MAZ	chr12:40617948-40619513	GM12878	blood:	n/a	chr12:40618784-40618793
13	GATA3	chr12:40618028-40618826	T-47D	breast:	n/a	chr12:40618106-40618116
14	MYC	chr12:40617939-40619195	NB4	blood:	n/a	chr12:40618784-40618793
15	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
16	GATA3	chr12:40617963-40618479	SH-SY5Y	brain:	n/a	chr12:40618106-40618116
17	WRNIP1	chr12:40617979-40618276	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
19	MAX	chr12:40618017-40619722	A549	lung:	n/a	chr12:40618784-40618793
20	POLR2A	chr12:40616903-40621176	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40615913..40618239-chr12:40619276..40621204,2	K562	blood:

Variant related genes	Relation type
LRRK2	TF binding region
ENSG00000225342	TF binding region
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10506143	1.00[JPT][hapmap]
rs10506144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10506146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10506147	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506154	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10878244	1.00[JPT][hapmap]
rs11175186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11175593	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11564117	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11564123	1.00[JPT][hapmap]
rs11564131	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11564145	1.00[CEU][hapmap]
rs11564152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11564153	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564185	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11564187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564190	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11564196	1.00[JPT][hapmap]
rs11564199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564209	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11564210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564212	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564214	1.00[AFR][1000 genomes]
rs11564216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11564218	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11564253	1.00[CEU][hapmap]
rs11564255	1.00[CEU][hapmap]
rs11564256	1.00[CEU][hapmap]
rs11564266	1.00[CEU][hapmap]
rs11564271	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12422390	1.00[CEU][hapmap]
rs12422544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12422796	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12423419	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs12423551	1.00[JPT][hapmap]
rs12423986	1.00[CEU][hapmap]
rs12424040	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12424294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12424424	1.00[CEU][hapmap]
rs12425561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12426378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12426639	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12426643	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12426903	1.00[CEU][hapmap]
rs12427022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12427134	1.00[CEU][hapmap]
rs12427245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1365768	1.00[CEU][hapmap]
rs1365769	1.00[CEU][hapmap]
rs1388585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1463717	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1491945	0.94[AMR][1000 genomes]
rs17442924	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443078	0.86[EUR][1000 genomes]
rs17443178	0.80[EUR][1000 genomes]
rs17443185	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443206	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443600	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17443656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17443909	0.87[EUR][1000 genomes]
rs17444028	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17444054	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17444103	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17444646	1.00[CEU][hapmap]
rs17444667	1.00[CEU][hapmap]
rs17444688	1.00[CEU][hapmap]
rs17444744	1.00[CEU][hapmap]
rs17444751	1.00[CEU][hapmap]
rs17458230	1.00[JPT][hapmap]
rs17458549	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17458808	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17461387	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17461575	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461664	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17465610	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17465946	0.87[EUR][1000 genomes]
rs17466016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17466626	1.00[CEU][hapmap]
rs17466907	1.00[CEU][hapmap]
rs17466969	1.00[CEU][hapmap]
rs17467039	1.00[CEU][hapmap]
rs17467081	1.00[CEU][hapmap]
rs17467088	1.00[CEU][hapmap]
rs17467102	1.00[CEU][hapmap]
rs17467116	1.00[CEU][hapmap]
rs17467137	1.00[CEU][hapmap]
rs17467144	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs17483919	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17484003	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17484141	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs17484342	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17484493	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17492152	1.00[CEU][hapmap]
rs2017917	1.00[CEU][hapmap]
rs2131081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2638223	0.86[EUR][1000 genomes]
rs2708460	0.86[EUR][1000 genomes]
rs28365169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28365173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28365206	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs28365229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28365689	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28370664	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28370682	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28370830	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34567498	0.80[AMR][1000 genomes]
rs36212067	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36220738	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3789329	1.00[CEU][hapmap]
rs3899331	1.00[CEU][hapmap]
rs4628750	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4767961	0.81[AMR][1000 genomes]
rs4767962	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4767964	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4767965	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768228	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768248	1.00[CEU][hapmap]
rs4768249	1.00[CEU][hapmap]
rs4768251	1.00[CEU][hapmap]
rs4768252	1.00[ASW][hapmap]
rs4768253	1.00[ASW][hapmap]
rs4768254	1.00[CEU][hapmap]
rs72547977	0.87[EUR][1000 genomes]
rs729215	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7485401	1.00[CEU][hapmap]
rs7487209	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40619200	Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
3	chr12:40616600-40619000	Active TSS	Primary B cells from peripheral blood	blood
4	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:40616800-40618800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
8	chr12:40617400-40618200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
9	chr12:40617400-40619000	Active TSS	Duodenum Mucosa	Duodenum
10	chr12:40617400-40619200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:40617400-40619400	Active TSS	Small Intestine	intestine
12	chr12:40617400-40619600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:40617400-40619800	Active TSS	NHDF-Ad	bronchial
14	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
15	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr12:40617400-40621000	Active TSS	Right Atrium	heart
19	chr12:40617400-40621400	Active TSS	Aorta	Aorta
20	chr12:40617600-40618200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:40617600-40618200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:40617600-40618200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
23	chr12:40617600-40619800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:40617600-40620200	Active TSS	Ovary	ovary
25	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
27	chr12:40617800-40618200	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr12:40617800-40618200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:40617800-40618200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:40617800-40618200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:40617800-40618200	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr12:40617800-40618200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr12:40617800-40618200	Bivalent Enhancer	Fetal Heart	heart
34	chr12:40617800-40618200	Flanking Active TSS	Fetal Stomach	stomach
35	chr12:40617800-40618400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr12:40617800-40618400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:40617800-40619000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:40617800-40619000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:40617800-40619000	Active TSS	Fetal Muscle Leg	muscle
40	chr12:40617800-40619200	Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr12:40617800-40619400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
42	chr12:40617800-40619400	Active TSS	NHLF	lung
43	chr12:40617800-40619600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr12:40617800-40619600	Active TSS	Right Ventricle	heart
45	chr12:40617800-40620000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
47	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
48	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
49	chr12:40618000-40618200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr12:40618000-40618200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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