Variant report

Variant	rs538237054
Chromosome Location	chr1:211431906-211431907
allele	C/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	BRCA1	chr1:211431529-211432901	Hela-S3	cervix:	n/a	n/a
2	SIN3AK20	chr1:211431590-211432109	K562	blood:	n/a	n/a
3	TEAD4	chr1:211431470-211433039	K562	blood:	n/a	n/a
4	SP1	chr1:211431619-211433120	HCT-116	colon:	n/a	chr1:211432561-211432575 chr1:211432556-211432570 chr1:211432543-211432552 chr1:211432547-211432559 chr1:211432562-211432571 chr1:211432549-211432558 chr1:211432548-211432562 chr1:211432547-211432559 chr1:211432885-211432894 chr1:211432548-211432558 chr1:211432544-211432553 chr1:211432543-211432557 chr1:211431792-211431804 chr1:211432543-211432552 chr1:211432548-211432557 chr1:211431793-211431807 chr1:211432886-211432899
5	EP300	chr1:211431486-211433010	GM12878	blood:	n/a	chr1:211431928-211431942 chr1:211431835-211431849 chr1:211431593-211431607 chr1:211432524-211432540 chr1:211432435-211432451
6	ELK1	chr1:211431906-211432904	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:211431656-211433335	GM15510	blood:	n/a	n/a
8	TEAD4	chr1:211431529-211432999	SK-N-SH	brain:	n/a	n/a
9	SIX5	chr1:211431554-211432407	A549	lung:	n/a	n/a
10	RELA	chr1:211431556-211432953	GM15510	blood:	n/a	chr1:211432536-211432545 chr1:211432536-211432545
11	TAF1	chr1:211431460-211433208	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFF	chr1:211431730-211432066	K562	blood:	n/a	n/a
13	RAD21	chr1:211431561-211431983	Hela-S3	cervix:	n/a	n/a
14	RELA	chr1:211431544-211433052	GM12891	blood:	n/a	chr1:211432536-211432545 chr1:211432536-211432545
15	TBL1XR1	chr1:211431587-211432919	K562	blood:	n/a	n/a
16	POLR2A	chr1:211431601-211431980	HepG2	liver:	n/a	n/a
17	ZNF143	chr1:211431635-211433046	GM12878	blood:	n/a	chr1:211432558-211432576
18	ETS1	chr1:211431681-211432990	A549	lung:	n/a	chr1:211432025-211432042 chr1:211431731-211431738
19	TBP	chr1:211431539-211433145	K562	blood:	n/a	n/a
20	MAFK	chr1:211430859-211432505	K562	blood:	n/a	chr1:211431508-211431525
21	MAX	chr1:211431886-211433145	ECC-1	luminal epithelium:	n/a	chr1:211432409-211432419 chr1:211432314-211432324
22	JUN	chr1:211431665-211433033	K562	blood:	n/a	chr1:211432319-211432328 chr1:211432316-211432325
23	UBTF	chr1:211431414-211434505	K562	blood:	n/a	n/a
24	CTCF	chr1:211431672-211431993	K562	blood:	n/a	n/a
25	CTCF	chr1:211431760-211431910	AG10803	skin:	n/a	n/a
26	MAX	chr1:211431551-211433316	K562	blood:	n/a	chr1:211432409-211432419 chr1:211432314-211432324
27	POLR2A	chr1:211431331-211433272	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr1:211431514-211432517	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr1:211431417-211433266	A549	lung:	n/a	chr1:211432409-211432419 chr1:211432314-211432324
30	CREB1	chr1:211431466-211432975	K562	blood:	n/a	n/a
31	POLR2A	chr1:211431511-211432536	GM12891	blood:	n/a	n/a
32	MXI1	chr1:211431485-211432559	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:211431419-211433532	H1-neurons	neurons:	n/a	n/a
34	CTCF	chr1:211431780-211431930	GM12864	blood:	n/a	n/a
35	PAX5	chr1:211431678-211431919	GM12891	blood:	n/a	chr1:211431840-211431849
36	TAF1	chr1:211431624-211431950	SK-N-SH	brain:	n/a	n/a
37	TCF12	chr1:211431361-211433146	A549	lung:	n/a	chr1:211431625-211431633
38	MAX	chr1:211431588-211433126	HepG2	liver:	n/a	chr1:211432409-211432419 chr1:211432314-211432324
39	MAZ	chr1:211431464-211434733	K562	blood:	n/a	chr1:211432409-211432419 chr1:211433819-211433829 chr1:211432314-211432324
40	MYC	chr1:211431167-211432603	MCF10A-Er-Src	breast:	n/a	chr1:211432409-211432419 chr1:211432314-211432324
41	MAX	chr1:211431566-211433295	HepG2	liver:	n/a	chr1:211432409-211432419 chr1:211432314-211432324
42	TBP	chr1:211431229-211432844	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr1:211431533-211433398	K562	blood:	n/a	n/a
44	HA-E2F1	chr1:211431874-211433089	MCF-7	breast:	n/a	chr1:211432325-211432334 chr1:211432426-211432438 chr1:211432426-211432437
45	ZMIZ1	chr1:211431466-211433049	K562	blood:	n/a	n/a
46	TAF1	chr1:211431612-211433419	ECC-1	luminal epithelium:	n/a	n/a
47	E2F6	chr1:211431628-211432755	A549	lung:	n/a	chr1:211432425-211432436 chr1:211432325-211432334 chr1:211432426-211432438
48	CTCF	chr1:211431860-211432010	WI-38	lung:	n/a	n/a
49	POLR2A	chr1:211431536-211434534	NB4	blood:	n/a	n/a
50	POLR2A	chr1:211431386-211432568	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210543442..210549646-chr1:211430130..211435518,10	MCF-7	breast:
2	chr1:211431380..211432214-chr14:75745176..75745718,2	Hela-S3	cervix:
3	chr1:211431689..211435313-chr1:211451941..211455577,4	K562	blood:
4	chr1:211431871..211432822-chr12:57984812..57985355,2	Hela-S3	cervix:
5	chr1:210545161..210548943-chr1:211431162..211434734,10	MCF-7	breast:
6	chr1:211429664..211434083-chr1:211498779..211503937,6	K562	blood:
7	chr1:211431812..211432720-chr3:20227589..20228353,2	Hela-S3	cervix:
8	chr1:211430859..211434419-chr1:211555069..211558654,5	K562	blood:
9	chr1:211429664..211435180-chr1:211498779..211503937,6	K562	blood:
10	chr1:211429991..211432106-chr1:211750411..211752434,2	MCF-7	breast:
11	chr1:211431809..211433608-chr1:212207599..212209157,2	K562	blood:
12	chr1:211431774..211432328-chr15:90895431..90896017,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH1-2	chr1:211431307-211431917	NONHSAT009281

Variant related genes	Relation type
RCOR3	TF binding region
ENSG00000200972	Chromatin interaction
ENSG00000196391	Chromatin interaction
ENSG00000153363	Chromatin interaction
ENSG00000082512	Chromatin interaction
ENSG00000170385	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000143493	Chromatin interaction
ENSG00000170345	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	esv3343270	chr1:211431354-211434202	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv3352231	chr1:211431654-211434427	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr1:211430600-211432200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:211430600-211432200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr1:211430600-211434600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:211430600-211434600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:211430800-211432000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr1:211430800-211432000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr1:211430800-211432000	Bivalent/Poised TSS	HepG2	liver
8	chr1:211430800-211432200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:211430800-211432200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:211430800-211432400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:211430800-211434600	Active TSS	Aorta	Aorta
12	chr1:211431000-211432000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:211431000-211432000	Active TSS	Brain Germinal Matrix	brain
14	chr1:211431000-211434400	Active TSS	Brain Anterior Caudate	brain
15	chr1:211431000-211434400	Active TSS	NHLF	lung
16	chr1:211431000-211434800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:211431000-211434800	Active TSS	Fetal Intestine Large	intestine
18	chr1:211431200-211432000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:211431200-211432200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:211431200-211432200	Flanking Active TSS	Osteobl	bone
21	chr1:211431200-211432400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr1:211431200-211432400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:211431200-211434200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:211431200-211434200	Active TSS	Fetal Muscle Trunk	muscle
25	chr1:211431200-211434200	Active TSS	Fetal Muscle Leg	muscle
26	chr1:211431200-211434400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:211431200-211434400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:211431200-211434400	Active TSS	Placenta Amnion	Placenta Amnion
29	chr1:211431200-211434600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:211431200-211434600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:211431200-211434600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr1:211431200-211434600	Active TSS	Fetal Stomach	stomach
33	chr1:211431200-211434600	Active TSS	K562	blood
34	chr1:211431200-211434800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:211431200-211434800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:211431200-211434800	Active TSS	Fetal Intestine Small	intestine
37	chr1:211431200-211435000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:211431400-211432000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr1:211431400-211432000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:211431400-211432200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:211431400-211432200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:211431400-211432200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr1:211431400-211432200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:211431400-211432400	Flanking Active TSS	HUVEC	blood vessel
45	chr1:211431400-211433800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:211431400-211434400	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr1:211431400-211434400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:211431400-211434400	Active TSS	Colonic Mucosa	Colon
49	chr1:211431400-211434400	Active TSS	Colon Smooth Muscle	Colon
50	chr1:211431400-211434400	Active TSS	Duodenum Smooth Muscle	Duodenum

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