Variant report

Variant	rs41313916
Chromosome Location	chr1:196577545-196577546
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	ATF2	chr1:196577288-196578552	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:196577097-196578630	H1-neurons	neurons:	n/a	n/a
3	EP300	chr1:196577407-196578422	H1-hESC	embryonic stem cell:	n/a	chr1:196577655-196577669
4	POLR2A	chr1:196577132-196578701	H1-hESC	embryonic stem cell:	n/a	n/a
5	GATA2	chr1:196577184-196578832	SH-SY5Y	brain:	n/a	chr1:196578008-196578021 chr1:196577813-196577824
6	ATF3	chr1:196577509-196577792	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr1:196577489-196577842	IMR90	lung:	n/a	n/a
8	ZNF143	chr1:196577284-196578739	H1-hESC	embryonic stem cell:	n/a	chr1:196577964-196577974
9	SIN3A	chr1:196576883-196578976	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr1:196577261-196578124	H1-hESC	embryonic stem cell:	n/a	chr1:196577722-196577732 chr1:196577890-196577902 chr1:196577890-196577900
11	TBP	chr1:196577168-196578784	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:196576870-196579084	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:196577266-196578277	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:196577186-196578788	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:196577110-196578236	PFSK-1	brain:	n/a	n/a
16	CHD1	chr1:196576411-196579113	H1-hESC	embryonic stem cell:	n/a	n/a
17	CEBPB	chr1:196577156-196578831	H1-hESC	embryonic stem cell:	n/a	chr1:196578044-196578052 chr1:196578654-196578665
18	YY1	chr1:196577084-196578590	H1-hESC	embryonic stem cell:	n/a	chr1:196577183-196577193 chr1:196577178-196577194
19	TAF1	chr1:196577219-196578598	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:196577317-196578175	Gliobla	brain:	n/a	n/a
21	POLR2A	chr1:196577449-196578466	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr1:196577332-196577789	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr1:196577164-196578228	H1-hESC	embryonic stem cell:	n/a	chr1:196577183-196577193 chr1:196577178-196577194
24	POLR2A	chr1:196577321-196578528	H1-neurons	neurons:	n/a	n/a
25	CHD2	chr1:196577189-196578907	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:196577216-196578669	H1-hESC	embryonic stem cell:	n/a	n/a
27	GTF2F1	chr1:196577287-196578625	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:196577466-196577889	U87	brain:	n/a	n/a
29	POLR2A	chr1:196577180-196578063	PFSK-1	brain:	n/a	n/a
30	JUND	chr1:196577323-196578645	H1-hESC	embryonic stem cell:	n/a	chr1:196578045-196578054 chr1:196577764-196577773 chr1:196578434-196578442
31	MAX	chr1:196577465-196578875	H1-hESC	embryonic stem cell:	n/a	chr1:196577658-196577667 chr1:196578657-196578666 chr1:196578159-196578169
32	TAF1	chr1:196577131-196578857	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:196577369-196578179	SK-N-MC	brain:	n/a	n/a
34	MXI1	chr1:196576771-196579339	SK-N-SH	brain:	n/a	n/a
35	RFX5	chr1:196576790-196579150	SK-N-SH	brain:	n/a	chr1:196578044-196578053
36	KAP1	chr1:196576920-196578640	U2OS	brain:	n/a	n/a
37	RAD21	chr1:196577163-196578048	SK-N-SH_RA	brain:	n/a	chr1:196577722-196577732 chr1:196577890-196577902 chr1:196577890-196577900
38	TAF7	chr1:196577280-196578126	H1-hESC	embryonic stem cell:	n/a	n/a
39	KAP1	chr1:196577054-196578853	HEK293	kidney:	n/a	n/a
40	RAD21	chr1:196577292-196578650	H1-hESC	embryonic stem cell:	n/a	chr1:196577722-196577732 chr1:196577890-196577902 chr1:196577890-196577900
41	TCF12	chr1:196577167-196577823	A549	lung:	n/a	n/a
42	CTBP2	chr1:196577115-196578779	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr1:196577368-196578832	H1-hESC	embryonic stem cell:	n/a	chr1:196577658-196577667 chr1:196578657-196578666 chr1:196578159-196578169
44	MAX	chr1:196577518-196578183	A549	lung:	n/a	chr1:196577658-196577667 chr1:196578159-196578169
45	MAX	chr1:196577496-196578705	H1-hESC	embryonic stem cell:	n/a	chr1:196577658-196577667 chr1:196578657-196578666 chr1:196578159-196578169
46	CREB1	chr1:196577517-196578682	H1-hESC	embryonic stem cell:	n/a	n/a
47	REST	chr1:196577016-196578861	H1-neurons	neurons:	n/a	chr1:196577534-196577541
48	MXI1	chr1:196577448-196578637	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr1:196577371-196578427	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
KCNT2	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs17700121	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv947214	chr1:196573327-196578627	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196574800-196578600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:196574800-196578800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:196575800-196578200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:196575800-196578400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:196575800-196578600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr1:196575800-196579200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:196576000-196578600	Active TSS	Ovary	ovary
8	chr1:196576000-196578600	Active TSS	Right Atrium	heart
9	chr1:196576200-196578000	Active TSS	Liver	Liver
10	chr1:196576200-196578400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:196576200-196578400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr1:196576200-196578400	Active TSS	Fetal Brain Male	brain
13	chr1:196576200-196578600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:196576200-196578800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:196576400-196578400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:196576400-196578400	Active TSS	Fetal Stomach	stomach
17	chr1:196576400-196578600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr1:196576400-196578800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:196576400-196579200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:196576600-196578200	Active TSS	Brain Germinal Matrix	brain
21	chr1:196576600-196578400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:196576600-196578400	Active TSS	Brain Angular Gyrus	brain
23	chr1:196576600-196578400	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:196576600-196578400	Active TSS	Fetal Kidney	kidney
25	chr1:196576600-196578600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:196576600-196578600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:196576600-196578600	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:196576800-196577600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:196576800-196577600	Active TSS	Duodenum Mucosa	Duodenum
30	chr1:196576800-196577600	Flanking Active TSS	HUVEC	blood vessel
31	chr1:196576800-196577800	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:196576800-196578000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
33	chr1:196576800-196578000	Active TSS	Fetal Muscle Leg	muscle
34	chr1:196576800-196578400	Active TSS	A549	lung
35	chr1:196576800-196578400	Active TSS	NHDF-Ad	bronchial
36	chr1:196576800-196578400	Active TSS	NHLF	lung
37	chr1:196576800-196578600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:196576800-196578600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:196576800-196578600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:196576800-196578600	Active TSS	Fetal Lung	lung
41	chr1:196576800-196578600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr1:196576800-196578600	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr1:196576800-196578800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:196576800-196578800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:196576800-196578800	Active TSS	Stomach Smooth Muscle	stomach
46	chr1:196577000-196577800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr1:196577000-196578000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:196577000-196578200	Active TSS	HSMM	muscle
49	chr1:196577000-196578200	Active TSS	HSMMtube	muscle
50	chr1:196577000-196578400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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