Variant report

Variant	rs12141363
Chromosome Location	chr1:47696581-47696582
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	E2F6	chr1:47696249-47696927	H1-hESC	embryonic stem cell:	n/a	chr1:47696590-47696601 chr1:47696589-47696601 chr1:47696593-47696600 chr1:47696593-47696600 chr1:47696593-47696600 chr1:47696592-47696601
2	ZMIZ1	chr1:47696433-47698351	K562	blood:	n/a	n/a
3	MAZ	chr1:47696025-47698451	K562	blood:	n/a	chr1:47697793-47697803 chr1:47697635-47697645 chr1:47696587-47696597
4	POLR2A	chr1:47696440-47696965	HUVEC	blood vessel:	n/a	n/a
5	TBL1XR1	chr1:47696042-47699626	K562	blood:	n/a	n/a
6	BACH1	chr1:47696054-47698375	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTBP2	chr1:47696143-47698399	H1-hESC	embryonic stem cell:	n/a	n/a
8	NR2F2	chr1:47696055-47699387	K562	blood:	n/a	n/a
9	JUN	chr1:47694131-47700215	K562	blood:	n/a	chr1:47697692-47697701
10	POLR2A	chr1:47696465-47698369	K562	blood:	n/a	n/a
11	YY1	chr1:47696447-47698333	K562	blood:	n/a	chr1:47697661-47697670 chr1:47697638-47697649 chr1:47697646-47697660 chr1:47696692-47696703 chr1:47698080-47698090 chr1:47697653-47697667 chr1:47697650-47697661 chr1:47697659-47697670
12	MAX	chr1:47696434-47698286	K562	blood:	n/a	chr1:47697793-47697803 chr1:47697635-47697645 chr1:47696587-47696597
13	POLR2A	chr1:47696089-47698429	K562	blood:	n/a	n/a
14	EP300	chr1:47696449-47698580	K562	blood:	n/a	chr1:47696694-47696703 chr1:47697551-47697565
15	POLR2A	chr1:47693272-47698475	K562	blood:	n/a	n/a
16	POLR2A	chr1:47695211-47698382	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr1:47695954-47698389	K562	blood:	n/a	n/a
18	POLR2A	chr1:47696006-47698386	K562	blood:	n/a	n/a
19	POLR2A	chr1:47693945-47698523	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:47694104-47698334	K562	blood:	n/a	n/a
21	GATA1	chr1:47691744-47699667	K562	blood:	n/a	chr1:47698033-47698046 chr1:47698035-47698045 chr1:47698037-47698044 chr1:47698026-47698043 chr1:47698035-47698044 chr1:47698037-47698047
22	MYC	chr1:47696520-47698451	K562	blood:	n/a	chr1:47697793-47697803 chr1:47697635-47697645 chr1:47696587-47696597
23	POLR2A	chr1:47694301-47698516	K562	blood:	n/a	n/a
24	CCNT2	chr1:47696493-47698508	K562	blood:	n/a	chr1:47698450-47698459 chr1:47698026-47698046
25	POLR2A	chr1:47696544-47698361	HUVEC	blood vessel:	n/a	n/a
26	E2F6	chr1:47696430-47698438	K562	blood:	n/a	chr1:47698060-47698069 chr1:47696590-47696601 chr1:47696589-47696601 chr1:47696593-47696600 chr1:47696593-47696600 chr1:47697644-47697654 chr1:47697647-47697657 chr1:47696593-47696600 chr1:47696592-47696601
27	POLR2A	chr1:47696569-47698344	K562	blood:	n/a	n/a
28	POLR2A	chr1:47694315-47698303	HUVEC	blood vessel:	n/a	n/a
29	STAT5A	chr1:47694213-47698426	K562	blood:	n/a	chr1:47697722-47697734 chr1:47695028-47695052 chr1:47697611-47697623 chr1:47697690-47697702 chr1:47698097-47698106 chr1:47698098-47698107
30	SUZ12	chr1:47695883-47697591	H1-hESC	embryonic stem cell:	n/a	n/a
31	CEBPD	chr1:47696526-47698441	K562	blood:	n/a	chr1:47697595-47697604
32	TAF1	chr1:47696423-47698404	K562	blood:	n/a	n/a
33	MAX	chr1:47696413-47698405	K562	blood:	n/a	chr1:47697793-47697803 chr1:47697635-47697645 chr1:47696587-47696597
34	SIN3A	chr1:47696473-47696885	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:47696460-47698353	K562	blood:	n/a	n/a
36	EGR1	chr1:47696423-47698291	K562	blood:	n/a	chr1:47696900-47696915 chr1:47697662-47697671 chr1:47697683-47697693 chr1:47696584-47696597 chr1:47696901-47696914 chr1:47697792-47697802 chr1:47697659-47697672 chr1:47697659-47697672 chr1:47696584-47696597 chr1:47697659-47697672
37	POLR2A	chr1:47691819-47699200	PBDE	blood:	n/a	n/a
38	YY1	chr1:47696462-47698278	K562	blood:	n/a	chr1:47697661-47697670 chr1:47697638-47697649 chr1:47697646-47697660 chr1:47696692-47696703 chr1:47698080-47698090 chr1:47697653-47697667 chr1:47697650-47697661 chr1:47697659-47697670
39	E2F4	chr1:47696519-47698369	K562	blood:	n/a	chr1:47698060-47698069 chr1:47696589-47696601 chr1:47696593-47696600 chr1:47696593-47696600 chr1:47697644-47697654 chr1:47697647-47697657 chr1:47696593-47696600 chr1:47696592-47696601
40	UBTF	chr1:47694227-47698484	K562	blood:	n/a	n/a
41	MYC	chr1:47696149-47698390	K562	blood:	n/a	chr1:47697793-47697803 chr1:47697635-47697645 chr1:47696587-47696597
42	EGR1	chr1:47696437-47698287	K562	blood:	n/a	chr1:47696900-47696915 chr1:47697662-47697671 chr1:47697683-47697693 chr1:47696584-47696597 chr1:47696901-47696914 chr1:47697792-47697802 chr1:47697659-47697672 chr1:47697659-47697672 chr1:47696584-47696597 chr1:47697659-47697672
43	E2F6	chr1:47696494-47696660	K562	blood:	n/a	chr1:47696590-47696601 chr1:47696589-47696601 chr1:47696593-47696600 chr1:47696593-47696600 chr1:47696593-47696600 chr1:47696592-47696601
44	ZC3H11A	chr1:47696520-47696585	K562	blood:	n/a	n/a
45	TBP	chr1:47696557-47698579	K562	blood:	n/a	n/a
46	TEAD4	chr1:47695855-47698535	K562	blood:	n/a	n/a
47	TAF1	chr1:47696497-47698337	K562	blood:	n/a	n/a
48	HEY1	chr1:47696439-47697900	K562	blood:	n/a	chr1:47697647-47697662 chr1:47696691-47696706 chr1:47697653-47697668
49	HMGN3	chr1:47696475-47698316	K562	blood:	n/a	n/a
50	POLR2A	chr1:47695220-47698260	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47696558..47698524-chr1:47778724..47781604,2	K562	blood:
2	chr1:47695487..47699315-chr1:47745491..47748993,3	K562	blood:
3	chr1:47696136..47700063-chr1:47798634..47802913,8	K562	blood:
4	chr1:47695872..47699054-chr1:47778639..47781604,5	K562	blood:
5	chr1:47696333..47699229-chr1:47798340..47801363,4	K562	blood:

Variant related genes	Relation type
TAL1	TF binding region
ENSG00000123473	Chromatin interaction
ENSG00000162368	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1015890	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789504	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890472	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211481	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211482	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12057184	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12083555	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12144626	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12407157	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543502	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1810658	0.83[AMR][1000 genomes]
rs2008713	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2984618	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34087210	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782665	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669341	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6695898	0.80[EUR][1000 genomes]
rs6700838	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701381	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs741959	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525145	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534271	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765861	1.00[ASN][1000 genomes]
rs7664	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs911910	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977747	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12141363	RP1-18D14.7	cis	Whole Blood	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47689800-47696600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:47690000-47697600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:47690200-47696800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:47692400-47696600	Weak transcription	Gastric	stomach
5	chr1:47693600-47697600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr1:47694200-47696600	Active TSS	Right Atrium	heart
7	chr1:47694200-47696600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
8	chr1:47694200-47697000	Active TSS	Lung	lung
9	chr1:47694200-47697200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr1:47694200-47697600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:47694400-47696600	Bivalent/Poised TSS	Placenta	Placenta
12	chr1:47694400-47697000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
13	chr1:47694400-47698600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr1:47694600-47698200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:47694800-47697200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr1:47694800-47697200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:47694800-47697200	Bivalent/Poised TSS	Colonic Mucosa	Colon
18	chr1:47695000-47696600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr1:47695000-47697000	Bivalent/Poised TSS	Liver	Liver
20	chr1:47695000-47697000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr1:47695000-47697200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
22	chr1:47695000-47697400	Bivalent/Poised TSS	Fetal Kidney	kidney
23	chr1:47695200-47696600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:47695200-47696800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
25	chr1:47695200-47697200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:47695200-47697200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:47695200-47697200	Active TSS	Right Ventricle	heart
28	chr1:47695400-47697000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
29	chr1:47695400-47697200	Bivalent/Poised TSS	Fetal Stomach	stomach
30	chr1:47695400-47697200	Bivalent/Poised TSS	Psoas Muscle	Psoas
31	chr1:47695400-47697400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:47695600-47696600	Weak transcription	Pancreas	Pancrea
33	chr1:47695600-47696600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
34	chr1:47695600-47697200	Bivalent/Poised TSS	Left Ventricle	heart
35	chr1:47695600-47697400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr1:47695600-47698200	Active TSS	HUVEC	blood vessel
37	chr1:47696000-47696600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
38	chr1:47696000-47696600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
39	chr1:47696000-47696800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:47696000-47697200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
41	chr1:47696000-47697200	Bivalent Enhancer	Brain Germinal Matrix	brain
42	chr1:47696200-47696600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:47696200-47696600	Bivalent/Poised TSS	Esophagus	oesophagus
44	chr1:47696200-47696600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
45	chr1:47696200-47696600	Enhancers	Spleen	Spleen
46	chr1:47696200-47696800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:47696200-47697000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
48	chr1:47696200-47697000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:47696200-47697200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr1:47696200-47697200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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