Variant report

Variant	rs3812841
Chromosome Location	chr13:38444350-38444351
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	TAF1	chr13:38444305-38444521	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr13:38444311-38444838	MCF-7	breast:	n/a	n/a
3	RAD21	chr13:38444251-38444845	H1-hESC	embryonic stem cell:	n/a	chr13:38444288-38444300
4	CTCF	chr13:38444307-38444843	MCF-7	breast:	n/a	chr13:38444579-38444600
5	CTCF	chr13:38444320-38444740	MCF-7	breast:	n/a	chr13:38444579-38444600
6	ZNF143	chr13:38444268-38444773	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr13:38444320-38444470	GM12868	blood:	n/a	n/a
8	POLR2A	chr13:38442597-38444770	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr13:38444215-38444706	MCF-7	breast:	n/a	chr13:38444254-38444267 chr13:38444579-38444600
10	SIN3AK20	chr13:38442808-38444759	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr13:38444278-38444698	MCF-7	breast:	n/a	chr13:38444579-38444600
12	ZNF263	chr13:38442968-38444874	HEK293-T-REx	kidney:	n/a	chr13:38443988-38443997
13	MAX	chr13:38443961-38444634	ECC-1	luminal epithelium:	n/a	n/a
14	MXI1	chr13:38444299-38444754	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr13:38444241-38444718	Fibrobl	skin:	n/a	chr13:38444254-38444267 chr13:38444579-38444600
16	CHD2	chr13:38442843-38444955	H1-hESC	embryonic stem cell:	n/a	n/a
17	KAP1	chr13:38444253-38445323	HEK293	kidney:	n/a	n/a
18	TBP	chr13:38444208-38445353	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr13:38444318-38444801	A549	lung:	n/a	n/a
20	CTCF	chr13:38444217-38444393	ProgFib	skin:	n/a	chr13:38444254-38444267
21	POLR2A	chr13:38443501-38444368	H1-neurons	neurons:	n/a	n/a
22	NFIC	chr13:38444060-38444769	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr13:38444132-38445448	H1-hESC	embryonic stem cell:	n/a	chr13:38444288-38444300
24	RAD21	chr13:38443832-38444801	IMR90	lung:	n/a	chr13:38443893-38443905 chr13:38444288-38444300
25	REST	chr13:38442575-38445418	H1-neurons	neurons:	n/a	chr13:38443382-38443396 chr13:38443882-38443900 chr13:38443384-38443394 chr13:38443403-38443411 chr13:38444081-38444094
26	RAD21	chr13:38442828-38445372	H1-hESC	embryonic stem cell:	n/a	chr13:38443893-38443905 chr13:38444288-38444300
27	MAX	chr13:38443615-38444827	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr13:38444307-38444913	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr13:38444320-38444723	K562	blood:	n/a	chr13:38444579-38444600
30	RAD21	chr13:38444186-38444855	ECC-1	luminal epithelium:	n/a	chr13:38444288-38444300
31	MAX	chr13:38443155-38444781	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr13:38443672-38444661	ProgFib	skin:	n/a	n/a
33	POLR2A	chr13:38444052-38444923	H1-neurons	neurons:	n/a	n/a
34	TAF1	chr13:38442785-38444720	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTBP2	chr13:38443161-38445209	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr13:38444346-38444768	HepG2	liver:	n/a	n/a
37	NFIC	chr13:38444055-38444667	ECC-1	luminal epithelium:	n/a	n/a
38	SIN3A	chr13:38442773-38445714	H1-hESC	embryonic stem cell:	n/a	chr13:38443787-38443800
39	POLR2A	chr13:38444013-38444395	MCF-7	breast:	n/a	n/a
40	POLR2A	chr13:38444045-38444481	MCF-7	breast:	n/a	n/a
41	POLR2A	chr13:38442825-38444634	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr13:38444290-38444705	MCF-7	breast:	n/a	chr13:38444579-38444600
43	CTCF	chr13:38444345-38444814	H1-hESC	embryonic stem cell:	n/a	chr13:38444579-38444600

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UFM1-1	chr13:38444084-38444803	XLOC_010350

Variant related genes	Relation type
TRPC4	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12584216	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1337601	0.80[AMR][1000 genomes]
rs1415601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1819607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812837	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3812840	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9532131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576388	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38440000-38444600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr13:38440400-38445000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:38440600-38445200	Active TSS	Fetal Brain Female	brain
4	chr13:38441000-38444600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr13:38441000-38444600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:38441400-38444600	Active TSS	NHDF-Ad	bronchial
7	chr13:38441600-38444600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:38441600-38444600	Active TSS	Osteobl	bone
9	chr13:38442000-38444600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:38442000-38444800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr13:38442200-38444600	Active TSS	NH-A	brain
12	chr13:38442200-38445200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr13:38442400-38444400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr13:38442400-38445200	Active TSS	Ovary	ovary
15	chr13:38442800-38444400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:38442800-38444400	Active TSS	Brain Anterior Caudate	brain
17	chr13:38442800-38444400	Active TSS	Fetal Kidney	kidney
18	chr13:38442800-38444400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
19	chr13:38442800-38444600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:38442800-38444600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:38442800-38444600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr13:38442800-38444600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:38442800-38444800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr13:38442800-38444800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr13:38442800-38444800	Active TSS	Brain Substantia Nigra	brain
26	chr13:38442800-38444800	Active TSS	Colon Smooth Muscle	Colon
27	chr13:38442800-38444800	Active TSS	Right Ventricle	heart
28	chr13:38442800-38445000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr13:38442800-38445200	Active TSS	Right Atrium	heart
30	chr13:38442800-38445400	Active TSS	Brain Angular Gyrus	brain
31	chr13:38443000-38444400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
32	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr13:38443000-38444600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr13:38443000-38444600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
37	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr13:38443000-38444600	Bivalent/Poised TSS	HSMMtube	muscle
39	chr13:38443000-38444800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr13:38443000-38444800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
41	chr13:38443000-38444800	Active TSS	Aorta	Aorta
42	chr13:38443000-38444800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
43	chr13:38443000-38444800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr13:38443000-38444800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
45	chr13:38443000-38445200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
46	chr13:38443200-38444400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr13:38443200-38444400	Flanking Bivalent TSS/Enh	Placenta	Placenta
48	chr13:38443200-38444400	Enhancers	Spleen	Spleen
49	chr13:38443200-38444600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr13:38443200-38444600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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