Variant report

Variant	rs6603975
Chromosome Location	chr1:92951239-92951240
allele	A/G
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	RUNX3	chr1:92949941-92952763	GM12878	blood:	n/a	chr1:92950835-92950850
2	SPI1	chr1:92951016-92952202	HL-60	blood:	n/a	n/a
3	MAX	chr1:92949938-92951680	ECC-1	luminal epithelium:	n/a	chr1:92949942-92949951 chr1:92951472-92951482
4	MAX	chr1:92951106-92951673	HepG2	liver:	n/a	chr1:92951472-92951482
5	EGR1	chr1:92950935-92951654	GM12878	blood:	n/a	chr1:92951290-92951300 chr1:92951485-92951498 chr1:92951523-92951533 chr1:92951486-92951495 chr1:92951485-92951498 chr1:92951074-92951084 chr1:92951286-92951300 chr1:92951523-92951536 chr1:92950956-92950969 chr1:92951480-92951502 chr1:92951485-92951498
6	BHLHE40	chr1:92950889-92951855	GM12878	blood:	n/a	chr1:92951281-92951297 chr1:92951364-92951380
7	POLR2A	chr1:92947404-92952793	GM19193	blood:	n/a	n/a
8	RELA	chr1:92950123-92952753	GM19193	blood:	n/a	n/a
9	POLR2A	chr1:92951012-92952743	HEK293	kidney:	n/a	n/a
10	POLR2A	chr1:92950859-92951905	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:92951158-92951626	GM12892	blood:	n/a	n/a
12	CHD1	chr1:92949844-92951923	GM12878	blood:	n/a	n/a
13	EP300	chr1:92950759-92951887	GM12878	blood:	n/a	chr1:92951165-92951181 chr1:92951445-92951461
14	MAX	chr1:92951128-92951624	K562	blood:	n/a	chr1:92951472-92951482
15	EGR1	chr1:92951066-92951784	ECC-1	luminal epithelium:	n/a	chr1:92951290-92951300 chr1:92951485-92951498 chr1:92951523-92951533 chr1:92951486-92951495 chr1:92951485-92951498 chr1:92951074-92951084 chr1:92951286-92951300 chr1:92951523-92951536 chr1:92951709-92951718 chr1:92951480-92951502 chr1:92951772-92951782 chr1:92951485-92951498
16	RCOR1	chr1:92950969-92951544	K562	blood:	n/a	n/a
17	EGR1	chr1:92951078-92951668	K562	blood:	n/a	chr1:92951290-92951300 chr1:92951485-92951498 chr1:92951523-92951533 chr1:92951486-92951495 chr1:92951485-92951498 chr1:92951286-92951300 chr1:92951523-92951536 chr1:92951480-92951502 chr1:92951485-92951498
18	POLR2A	chr1:92950807-92951921	HCT-116	colon:	n/a	n/a
19	MXI1	chr1:92950052-92951962	GM12878	blood:	n/a	n/a
20	ATF2	chr1:92951154-92951985	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:92951208-92951497	MCF-7	breast:	n/a	n/a
22	MAZ	chr1:92950794-92951847	K562	blood:	n/a	chr1:92951472-92951482
23	POLR2A	chr1:92948302-92953063	GM12878	blood:	n/a	n/a
24	CTBP2	chr1:92947650-92951849	H1-hESC	embryonic stem cell:	n/a	n/a
25	BACH1	chr1:92950462-92951930	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:92949981-92951931	GM12878	blood:	n/a	n/a
27	RELA	chr1:92950111-92951944	GM18951	blood:	n/a	n/a
28	RCOR1	chr1:92950677-92951891	GM12878	blood:	n/a	n/a
29	CTCF	chr1:92951200-92951335	GM12891	blood:	n/a	n/a
30	SUZ12	chr1:92945372-92953085	NT2-D1	testis:	n/a	n/a
31	CTCF	chr1:92951180-92951330	HVMF	connective:	n/a	n/a
32	ZNF143	chr1:92949952-92951877	GM12878	blood:	n/a	chr1:92950430-92950448 chr1:92950448-92950458
33	ZNF263	chr1:92949056-92952006	HEK293-T-REx	kidney:	n/a	chr1:92949398-92949407 chr1:92951239-92951248 chr1:92949255-92949264 chr1:92949422-92949431
34	POLR2A	chr1:92949883-92952028	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:92947650-92952772	GM18951	blood:	n/a	n/a
36	POLR2A	chr1:92950217-92951943	HepG2	liver:	n/a	n/a
37	ELF1	chr1:92947785-92952063	GM12878	blood:	n/a	chr1:92949334-92949343 chr1:92949903-92949915 chr1:92949809-92949821 chr1:92951584-92951596
38	TCF3	chr1:92951081-92951549	GM12878	blood:	n/a	chr1:92951451-92951464 chr1:92951283-92951296
39	BRCA1	chr1:92951204-92951349	GM12878	blood:	n/a	n/a
40	RUNX3	chr1:92950618-92952049	GM12878	blood:	n/a	chr1:92950835-92950850
41	EGR1	chr1:92950032-92952031	HCT-116	colon:	n/a	chr1:92951290-92951300 chr1:92951485-92951498 chr1:92950289-92950303 chr1:92951523-92951533 chr1:92951486-92951495 chr1:92951485-92951498 chr1:92951074-92951084 chr1:92951286-92951300 chr1:92951523-92951536 chr1:92950956-92950969 chr1:92951709-92951718 chr1:92951480-92951502 chr1:92951772-92951782 chr1:92951485-92951498
42	POLR2A	chr1:92947824-92952778	GM18505	blood:	n/a	n/a
43	CTCF	chr1:92950293-92951902	GM12878	blood:	n/a	chr1:92950459-92950467 chr1:92951365-92951378 chr1:92951524-92951537 chr1:92951530-92951539
44	POLR2A	chr1:92945762-92951903	H1-neurons	neurons:	n/a	n/a
45	ZEB1	chr1:92950595-92952074	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:92951133-92951882	GM12892	blood:	n/a	n/a
47	FOXM1	chr1:92950691-92951905	GM12878	blood:	n/a	n/a
48	BCLAF1	chr1:92950824-92951774	GM12878	blood:	n/a	chr1:92951518-92951531 chr1:92951284-92951297 chr1:92951516-92951529
49	MTA3	chr1:92949554-92952767	GM12878	blood:	n/a	n/a
50	EGR1	chr1:92951213-92951641	H1-hESC	embryonic stem cell:	n/a	chr1:92951290-92951300 chr1:92951485-92951498 chr1:92951523-92951533 chr1:92951486-92951495 chr1:92951485-92951498 chr1:92951286-92951300 chr1:92951523-92951536 chr1:92951480-92951502 chr1:92951485-92951498

Variant related genes	Relation type
GFI1	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1034219	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10465754	0.90[EUR][1000 genomes]
rs10465756	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10735778	0.90[EUR][1000 genomes]
rs10735779	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10747444	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10782922	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10782935	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10874656	0.98[EUR][1000 genomes]
rs10874712	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164605	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164654	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164770	0.82[EUR][1000 genomes]
rs11164773	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12753280	0.89[EUR][1000 genomes]
rs1408916	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1556562	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1556563	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1570836	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1570837	0.92[EUR][1000 genomes]
rs17579779	0.89[EUR][1000 genomes]
rs1886682	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1886683	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2025607	0.83[EUR][1000 genomes]
rs2031494	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2151577	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2184193	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2391159	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2391160	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4375281	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4568842	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4847181	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4847377	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4970696	0.97[EUR][1000 genomes]
rs4970698	0.97[EUR][1000 genomes]
rs4970701	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4970705	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4970706	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4970708	0.93[EUR][1000 genomes]
rs4970709	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4970710	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4970712	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59679370	0.89[EUR][1000 genomes]
rs6422512	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6422513	0.92[EUR][1000 genomes]
rs6422514	0.81[EUR][1000 genomes]
rs6603979	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6603980	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6603981	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6603982	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6603984	0.92[EUR][1000 genomes]
rs6603985	0.92[EUR][1000 genomes]
rs6603987	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6603988	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6603990	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6656432	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6661134	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6676141	0.83[EUR][1000 genomes]
rs6676846	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6686702	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6690764	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6692187	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6696173	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7515577	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7518357	0.88[EUR][1000 genomes]
rs7536295	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7552212	0.82[EUR][1000 genomes]
rs912795	0.97[EUR][1000 genomes]
rs962221	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs962222	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs989653	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv523354	chr1:92931263-93064823	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv3421594	chr1:92950889-92953737	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92945600-92952200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:92945600-92952600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:92945600-92952800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr1:92945800-92951800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:92946000-92952000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:92946600-92952000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
7	chr1:92947000-92951800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
8	chr1:92947000-92952000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
9	chr1:92947200-92951600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:92947400-92952000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
11	chr1:92947400-92952600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:92947600-92952000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr1:92947600-92952000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
14	chr1:92947600-92952000	Flanking Bivalent TSS/Enh	Placenta	Placenta
15	chr1:92947600-92952200	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:92947600-92952400	Active TSS	Thymus	Thymus
17	chr1:92947800-92951600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:92947800-92952000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:92947800-92952000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
20	chr1:92947800-92952600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
21	chr1:92948000-92952000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:92948000-92952600	Bivalent/Poised TSS	Small Intestine	intestine
23	chr1:92948000-92952800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr1:92948200-92952000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
25	chr1:92948200-92952600	Bivalent Enhancer	Fetal Brain Male	brain
26	chr1:92948400-92952600	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:92948400-92953000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:92948600-92952200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:92948600-92952600	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr1:92948600-92952800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:92948800-92952000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:92949000-92953000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:92949200-92952000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:92949200-92953400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr1:92949600-92951400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:92949600-92951800	Flanking Bivalent TSS/Enh	HMEC	breast
37	chr1:92949600-92952000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:92949800-92951600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
39	chr1:92949800-92951600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr1:92949800-92951600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
41	chr1:92949800-92951600	Flanking Active TSS	Spleen	Spleen
42	chr1:92949800-92952000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr1:92949800-92952000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:92949800-92952000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:92949800-92952000	Flanking Bivalent TSS/Enh	Left Ventricle	heart
46	chr1:92949800-92952000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr1:92949800-92952000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
48	chr1:92949800-92952400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:92950000-92951400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
50	chr1:92950000-92951800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--

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