Variant report

Variant	rs562989479
Chromosome Location	chr1:165797977-165797978
allele	G/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	chr1:165796617-165798455	Hela-S3	cervix:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
2	HEY1	chr1:165796685-165798591	HepG2	liver:	n/a	chr1:165797282-165797297 chr1:165797294-165797309 chr1:165796793-165796808 chr1:165797609-165797624 chr1:165797010-165797025 chr1:165797590-165797605 chr1:165797178-165797193 chr1:165797231-165797246
3	POLR2A	chr1:165796567-165798533	H1-neurons	neurons:	n/a	n/a
4	TBP	chr1:165797407-165799044	Hela-S3	cervix:	n/a	n/a
5	TBP	chr1:165796682-165798882	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr1:165795790-165799461	SK-N-SH	brain:	n/a	n/a
7	E2F4	chr1:165797415-165798603	MCF10A-Er-Src	breast:	n/a	chr1:165797655-165797666 chr1:165797654-165797666 chr1:165798240-165798251 chr1:165798235-165798250
8	ZBTB7A	chr1:165797039-165798063	K562	blood:	n/a	n/a
9	RAD21	chr1:165796693-165798782	IMR90	lung:	n/a	chr1:165797262-165797276 chr1:165796971-165796985
10	MAX	chr1:165796594-165798524	MCF-7	breast:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
11	ELF1	chr1:165796741-165798063	K562	blood:	n/a	chr1:165797231-165797243 chr1:165796961-165796970 chr1:165797175-165797187 chr1:165797276-165797288 chr1:165796773-165796782 chr1:165797819-165797830 chr1:165797611-165797623 chr1:165796948-165796960
12	POLR2A	chr1:165796642-165798540	GM19193	blood:	n/a	n/a
13	TAF1	chr1:165796552-165798793	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:165796740-165798427	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:165796575-165798518	HCT-116	colon:	n/a	n/a
16	STAT3	chr1:165797435-165798357	MCF10A-Er-Src	breast:	n/a	chr1:165797993-165798000 chr1:165797470-165797482 chr1:165798191-165798199 chr1:165797465-165797477
17	MYC	chr1:165796700-165798428	K562	blood:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
18	POLR2A	chr1:165796535-165798587	HUVEC	blood vessel:	n/a	n/a
19	MAX	chr1:165796657-165798487	HUVEC	blood vessel:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
20	MAX	chr1:165796762-165798850	K562	blood:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
21	ZNF263	chr1:165796775-165798907	HEK293-T-REx	kidney:	n/a	chr1:165797048-165797057 chr1:165798757-165798766
22	CHD1	chr1:165796796-165798733	H1-hESC	embryonic stem cell:	n/a	chr1:165797014-165797024 chr1:165797585-165797595 chr1:165797665-165797675
23	MAX	chr1:165796628-165798870	Hela-S3	cervix:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
24	POLR2A	chr1:165796598-165798503	ProgFib	skin:	n/a	n/a
25	GTF2B	chr1:165796815-165798441	K562	blood:	n/a	n/a
26	ELK1	chr1:165797590-165798258	K562	blood:	n/a	n/a
27	MAX	chr1:165796540-165798644	HepG2	liver:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
28	TBP	chr1:165796690-165798550	HepG2	liver:	n/a	n/a
29	YY1	chr1:165796676-165798459	GM12878	blood:	n/a	chr1:165797592-165797606 chr1:165798301-165798313 chr1:165797628-165797642 chr1:165797231-165797245 chr1:165796773-165796782 chr1:165797230-165797244 chr1:165797281-165797295 chr1:165797611-165797625
30	POLR2A	chr1:165797754-165798015	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr1:165796463-165798522	PFSK-1	brain:	n/a	n/a
32	MXI1	chr1:165796090-165799083	IMR90	lung:	n/a	n/a
33	HEY1	chr1:165796674-165798516	HepG2	liver:	n/a	chr1:165797282-165797297 chr1:165797294-165797309 chr1:165796793-165796808 chr1:165797609-165797624 chr1:165797010-165797025 chr1:165797590-165797605 chr1:165797178-165797193 chr1:165797231-165797246
34	MAX	chr1:165796559-165798551	SK-N-SH	brain:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
35	TAF1	chr1:165796629-165798520	PFSK-1	brain:	n/a	n/a
36	CHD2	chr1:165796722-165798524	K562	blood:	n/a	chr1:165797014-165797024 chr1:165796765-165796775 chr1:165797585-165797595 chr1:165797665-165797675
37	MYC	chr1:165796582-165798605	Hela-S3	cervix:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
38	TAF1	chr1:165796656-165798537	K562	blood:	n/a	n/a
39	MAX	chr1:165796582-165798547	H1-hESC	embryonic stem cell:	n/a	chr1:165797265-165797275 chr1:165797265-165797274 chr1:165797265-165797272
40	TAF1	chr1:165796524-165798600	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr1:165796606-165798547	GM18526	blood:	n/a	n/a
42	YY1	chr1:165797967-165798500	K562	blood:	n/a	chr1:165798301-165798313
43	POLR2A	chr1:165796642-165798967	GM12891	blood:	n/a	n/a
44	RUNX3	chr1:165796635-165798493	GM12878	blood:	n/a	n/a
45	YY1	chr1:165797907-165798498	SK-N-SH_RA	brain:	n/a	chr1:165798301-165798313
46	SIN3AK20	chr1:165797802-165798427	A549	lung:	n/a	n/a
47	STAT3	chr1:165797497-165798527	MCF10A-Er-Src	breast:	n/a	chr1:165797993-165798000 chr1:165798462-165798473 chr1:165798191-165798199
48	CUX1	chr1:165797760-165799023	K562	blood:	n/a	n/a
49	POLR2A	chr1:165796689-165798399	HCT-116	colon:	n/a	n/a
50	E2F1	chr1:165796632-165798438	Hela-S3	cervix:	n/a	chr1:165797654-165797666 chr1:165797013-165797022 chr1:165797007-165797016 chr1:165798240-165798251 chr1:165797654-165797665 chr1:165798235-165798250 chr1:165796975-165796985

No.	Distal block	Cell Line	Cell type
1	chr1:165685761..165688091-chr1:165797394..165800120,2	K562	blood:
2	chr1:165797619..165798446-chr10:35415749..35416742,2	Hela-S3	cervix:
3	chr1:165701898..165704747-chr1:165797455..165798967,2	K562	blood:
4	chr1:165710113..165712004-chr1:165797069..165798776,2	K562	blood:
5	chr1:165797297..165798088-chr19:893323..894173,2	Hela-S3	cervix:
6	chr1:165797353..165798141-chr14:103540442..103541389,2	Hela-S3	cervix:
7	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
8	chr1:165666837..165669027-chr1:165796687..165798880,2	MCF-7	breast:
9	chr1:165699126..165701487-chr1:165797315..165798954,2	K562	blood:
10	chr1:165795600..165798299-chr1:165863664..165866486,4	MCF-7	breast:
11	chr1:165797467..165799152-chr1:165835828..165838379,2	MCF-7	breast:
12	chr1:165741744..165743826-chr1:165797591..165799642,2	MCF-7	breast:
13	chr1:165599775..165601444-chr1:165795750..165798255,2	K562	blood:
14	chr1:165778822..165780861-chr1:165797146..165799667,2	MCF-7	breast:
15	chr1:165797729..165798599-chr15:82554332..82555042,2	Hela-S3	cervix:
16	chr1:165735066..165739781-chr1:165794447..165799093,13	MCF-7	breast:
17	chr1:165797029..165799386-chr1:165863557..165867019,3	K562	blood:
18	chr1:165797500..165798067-chr6:134489786..134490486,2	Hela-S3	cervix:
19	chr1:165797895..165798858-chr1:210546984..210547752,2	Hela-S3	cervix:
20	chr1:165797726..165798688-chr9:140135624..140136134,2	Hela-S3	cervix:
21	chr1:165797327..165800051-chr1:165876668..165879627,3	MCF-7	breast:
22	chr1:165797802..165798336-chr19:36036615..36037222,2	Hela-S3	cervix:
23	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
24	chr1:165797906..165798776-chr17:43225882..43226503,2	Hela-S3	cervix:
25	chr1:165797761..165798556-chr2:55275797..55276425,2	Hela-S3	cervix:
26	chr1:165797276..165798002-chr7:100860513..100861460,2	Hela-S3	cervix:
27	chr1:165598807..165601582-chr1:165797127..165800019,4	K562	blood:
28	chr1:165738181..165738790-chr1:165797712..165798704,2	Hela-S3	cervix:
29	chr1:165797822..165798445-chr11:65238400..65239297,2	Hela-S3	cervix:
30	chr1:165796719..165798432-chr1:167188997..167191733,2	K562	blood:
31	chr1:165795260..165799386-chr1:165863983..165867487,4	K562	blood:
32	chr1:165564921..165568209-chr1:165795710..165798284,3	K562	blood:
33	chr1:165736523..165741866-chr1:165791420..165802380,26	K562	blood:
34	chr1:165598109..165601268-chr1:165795469..165798298,3	MCF-7	breast:
35	chr1:165797659..165798365-chr7:50859677..50860628,2	Hela-S3	cervix:
36	chr1:165797268..165798031-chr11:64084976..64085603,2	Hela-S3	cervix:

Variant related genes	Relation type
TMCO1	TF binding region
ENSG00000140598	Chromatin interaction
ENSG00000126432	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000106400	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000230534	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000143190	Chromatin interaction
ENSG00000106397	Chromatin interaction
ENSG00000272205	Chromatin interaction
ENSG00000173113	Chromatin interaction
ENSG00000095794	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000236206	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000207507	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000143149	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv517792	chr1:165785503-165811729	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
4	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3357226	chr1:165795953-165798501	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a
6	nsv818544	chr1:165797966-165811729	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
7	nsv548097	chr1:165797966-165825166	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165796000-165798800	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr1:165796000-165799200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:165796200-165798000	Active TSS	Colonic Mucosa	Colon
4	chr1:165796200-165798000	Active TSS	Fetal Muscle Trunk	muscle
5	chr1:165796200-165798000	Active TSS	Right Ventricle	heart
6	chr1:165796200-165798600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:165796200-165798600	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:165796200-165798600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:165796200-165798600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:165796200-165798600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:165796200-165798600	Active TSS	Rectal Smooth Muscle	rectum
12	chr1:165796200-165798800	Active TSS	Aorta	Aorta
13	chr1:165796200-165798800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:165796200-165798800	Active TSS	NHDF-Ad	bronchial
15	chr1:165796200-165799000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:165796200-165799000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:165796200-165799200	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:165796400-165798000	Active TSS	Fetal Muscle Leg	muscle
19	chr1:165796400-165798200	Active TSS	Left Ventricle	heart
20	chr1:165796400-165798200	Active TSS	Placenta Amnion	Placenta Amnion
21	chr1:165796400-165798400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:165796400-165798400	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr1:165796400-165798600	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:165796400-165798600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:165796400-165798600	Active TSS	Brain Anterior Caudate	brain
26	chr1:165796400-165798600	Active TSS	Brain Germinal Matrix	brain
27	chr1:165796400-165798600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:165796400-165798600	Active TSS	Fetal Lung	lung
29	chr1:165796400-165798600	Active TSS	Thymus	Thymus
30	chr1:165796400-165798800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr1:165796400-165798800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:165796400-165798800	Active TSS	Fetal Kidney	kidney
33	chr1:165796400-165798800	Active TSS	Ovary	ovary
34	chr1:165796400-165799000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:165796400-165799000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:165796400-165799000	Active TSS	Fetal Intestine Large	intestine
37	chr1:165796400-165799200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr1:165796400-165799200	Active TSS	GM12878-XiMat	blood
39	chr1:165796400-165799400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:165796400-165799400	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:165796400-165799400	Active TSS	HSMMtube	muscle
42	chr1:165796400-165800000	Active TSS	Psoas Muscle	Psoas
43	chr1:165796600-165798000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr1:165796600-165798000	Active TSS	Adipose Nuclei	Adipose
45	chr1:165796600-165798000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:165796600-165798200	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr1:165796600-165798200	Active TSS	Brain Angular Gyrus	brain
48	chr1:165796600-165798200	Active TSS	Brain Substantia Nigra	brain
49	chr1:165796600-165798400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr1:165796600-165798400	Active TSS	Cortex derived primary cultured neurospheres	brain

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