Variant report

Variant	rs3812840
Chromosome Location	chr13:38444482-38444483
allele	C/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	TAF1	chr13:38444305-38444521	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr13:38444420-38444570	GM12866	blood:	n/a	n/a
3	RAD21	chr13:38444311-38444838	MCF-7	breast:	n/a	n/a
4	RAD21	chr13:38444251-38444845	H1-hESC	embryonic stem cell:	n/a	chr13:38444288-38444300
5	CTCF	chr13:38444307-38444843	MCF-7	breast:	n/a	chr13:38444579-38444600
6	CTCF	chr13:38444320-38444740	MCF-7	breast:	n/a	chr13:38444579-38444600
7	CTCF	chr13:38444411-38444778	GM12878	blood:	n/a	chr13:38444579-38444600
8	ZNF143	chr13:38444268-38444773	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr13:38444477-38444669	Pancreas_OC	pancreas:	n/a	chr13:38444579-38444600
10	RAD21	chr13:38444451-38444732	K562	blood:	n/a	n/a
11	CTCF	chr13:38444480-38444630	AoAF	blood vessel:	n/a	chr13:38444579-38444600
12	MAZ	chr13:38444402-38444672	K562	blood:	n/a	n/a
13	CTCF	chr13:38444480-38444630	GM12872	blood:	n/a	chr13:38444579-38444600
14	JUND	chr13:38444358-38444961	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr13:38442597-38444770	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr13:38444352-38444864	ECC-1	luminal epithelium:	n/a	n/a
17	RAD21	chr13:38444449-38444703	HepG2	liver:	n/a	n/a
18	SMC3	chr13:38444419-38444993	K562	blood:	n/a	n/a
19	CTCF	chr13:38444460-38444610	HFF-Myc	foreskin:	n/a	chr13:38444579-38444600
20	CTCF	chr13:38444215-38444706	MCF-7	breast:	n/a	chr13:38444254-38444267 chr13:38444579-38444600
21	MAX	chr13:38444445-38445454	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr13:38444380-38444530	WI-38	lung:	n/a	n/a
23	CTCF	chr13:38444480-38444630	GM12870	blood:	n/a	chr13:38444579-38444600
24	CTCF	chr13:38444464-38444682	K562	blood:	n/a	chr13:38444579-38444600
25	SIN3AK20	chr13:38442808-38444759	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr13:38444480-38444630	NHDF-neo	bronchial:	n/a	chr13:38444579-38444600
27	CTCF	chr13:38444278-38444698	MCF-7	breast:	n/a	chr13:38444579-38444600
28	CTCF	chr13:38444480-38444630	NHEK	skin:	n/a	chr13:38444579-38444600
29	CTCF	chr13:38444389-38444747	K562	blood:	n/a	chr13:38444579-38444600
30	CTCF	chr13:38444480-38444630	BJ	skin:	n/a	chr13:38444579-38444600
31	CTCF	chr13:38444432-38444717	Gliobla	brain:	n/a	chr13:38444579-38444600
32	ZNF263	chr13:38442968-38444874	HEK293-T-REx	kidney:	n/a	chr13:38443988-38443997
33	MAX	chr13:38443961-38444634	ECC-1	luminal epithelium:	n/a	n/a
34	MXI1	chr13:38444299-38444754	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr13:38444241-38444718	Fibrobl	skin:	n/a	chr13:38444254-38444267 chr13:38444579-38444600
36	CHD2	chr13:38442843-38444955	H1-hESC	embryonic stem cell:	n/a	n/a
37	CHD1	chr13:38444410-38444568	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr13:38444400-38444550	HAc	cerebellar:	n/a	n/a
39	CTCF	chr13:38444480-38444630	GM12864	blood:	n/a	chr13:38444579-38444600
40	CTCF	chr13:38444436-38444710	LNCaP	prostate:	n/a	chr13:38444579-38444600
41	CTCF	chr13:38444480-38444630	GM12873	blood:	n/a	chr13:38444579-38444600
42	KAP1	chr13:38444253-38445323	HEK293	kidney:	n/a	n/a
43	CTCF	chr13:38444460-38444610	GM06990	blood:	n/a	chr13:38444579-38444600
44	CTCF	chr13:38444480-38444630	BE2_C	brain:	n/a	chr13:38444579-38444600
45	MYC	chr13:38444415-38444632	K562	blood:	n/a	n/a
46	RAD21	chr13:38444479-38444685	GM12878	blood:	n/a	n/a
47	CTCF	chr13:38444480-38444630	HCM	heart:	n/a	chr13:38444579-38444600
48	CTCF	chr13:38444440-38444590	GM12864	blood:	n/a	n/a
49	TBP	chr13:38444208-38445353	H1-hESC	embryonic stem cell:	n/a	n/a
50	BACH1	chr13:38444435-38445233	H1-hESC	embryonic stem cell:	n/a	n/a

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: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12584216	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12874874	0.91[MEX][hapmap]
rs1337601	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1415601	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1538146	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1577876	0.91[MEX][hapmap]
rs17272200	0.91[MEX][hapmap]
rs1819607	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs1924379	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3812837	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3812841	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]
rs942345	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9532131	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548066	0.91[MEX][hapmap]
rs9548076	0.91[MEX][hapmap]
rs9548078	0.91[MEX][hapmap]
rs9576388	0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[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:91 , 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	chr13:38442400-38445200	Active TSS	Ovary	ovary
14	chr13:38442800-38444600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr13:38442800-38444600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:38442800-38444600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr13:38442800-38444600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:38442800-38444800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr13:38442800-38444800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr13:38442800-38444800	Active TSS	Brain Substantia Nigra	brain
21	chr13:38442800-38444800	Active TSS	Colon Smooth Muscle	Colon
22	chr13:38442800-38444800	Active TSS	Right Ventricle	heart
23	chr13:38442800-38445000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr13:38442800-38445200	Active TSS	Right Atrium	heart
25	chr13:38442800-38445400	Active TSS	Brain Angular Gyrus	brain
26	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr13:38443000-38444600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
30	chr13:38443000-38444600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
31	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr13:38443000-38444600	Bivalent/Poised TSS	HSMMtube	muscle
33	chr13:38443000-38444800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr13:38443000-38444800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr13:38443000-38444800	Active TSS	Aorta	Aorta
36	chr13:38443000-38444800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
37	chr13:38443000-38444800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
38	chr13:38443000-38444800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
39	chr13:38443000-38445200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr13:38443200-38444600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr13:38443200-38444600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr13:38443200-38444600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr13:38443200-38444600	Bivalent/Poised TSS	Left Ventricle	heart
44	chr13:38443200-38444800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr13:38443200-38444800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr13:38443200-38444800	Active TSS	K562	blood
47	chr13:38443200-38445400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:38443400-38444600	Flanking Bivalent TSS/Enh	NHEK	skin
49	chr13:38443400-38444800	Bivalent/Poised TSS	Psoas Muscle	Psoas
50	chr13:38443400-38445400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain

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