Variant report

Variant	rs3747615
Chromosome Location	chr1:159898100-159898101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:159898009-159898259	GM12878	blood:	n/a	n/a
2	EBF1	chr1:159897389-159898393	GM12878	blood:	n/a	chr1:159897622-159897633
3	CTCF	chr1:159898000-159898150	HBMEC	blood vessel:	n/a	n/a
4	CTCF	chr1:159897980-159898130	HepG2	liver:	n/a	n/a
5	CTCF	chr1:159897960-159898110	HMEC	breast:	n/a	n/a
6	CTCF	chr1:159897980-159898130	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr1:159897927-159898257	K562	blood:	n/a	n/a
8	CTCF	chr1:159898040-159898190	HAc	cerebellar:	n/a	n/a
9	ZBTB7A	chr1:159897932-159898115	K562	blood:	n/a	n/a
10	CTCF	chr1:159897960-159898110	HMF	breast:	n/a	n/a
11	RUNX3	chr1:159897457-159898161	GM12878	blood:	n/a	n/a
12	CTCF	chr1:159898000-159898150	AG04449	skin:	n/a	n/a
13	CTCF	chr1:159897980-159898130	BJ	skin:	n/a	n/a
14	CTCF	chr1:159897960-159898110	GM12867	blood:	n/a	n/a
15	CTCF	chr1:159898020-159898170	HA-sp	spinal cord:	n/a	n/a
16	CTCF	chr1:159897960-159898110	HCM	heart:	n/a	n/a
17	TCF12	chr1:159897914-159898160	GM12878	blood:	n/a	n/a
18	CTCF	chr1:159897980-159898130	K562	blood:	n/a	n/a
19	CTCF	chr1:159897928-159898169	K562	blood:	n/a	n/a
20	CTCF	chr1:159897960-159898110	AG09309	skin:	n/a	n/a
21	CTCF	chr1:159897902-159898173	GM12878	blood:	n/a	n/a
22	CTCF	chr1:159897960-159898110	GM12875	blood:	n/a	n/a
23	MAZ	chr1:159897983-159898124	GM12878	blood:	n/a	n/a
24	CTCF	chr1:159898000-159898150	HEK293	kidney:	n/a	n/a
25	CTCF	chr1:159898000-159898150	GM12874	blood:	n/a	n/a
26	ELF1	chr1:159897795-159898485	GM12878	blood:	n/a	n/a
27	CTCF	chr1:159897960-159898110	GM06990	blood:	n/a	n/a
28	CTCF	chr1:159897980-159898130	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:159896799..159899500-chr1:160000053..160002131,2	K562	blood:
2	chr1:159896747..159899727-chr1:160066907..160069830,2	K562	blood:
3	chr1:159849524..159855838-chr1:159893211..159898295,8	MCF-7	breast:

No data

Variant related genes	Relation type
TAGLN2	TF binding region
ENSG00000162729	Chromatin interaction
ENSG00000213085	Chromatin interaction
ENSG00000143315	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10752633	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13052	0.82[ASN][1000 genomes]
rs7543462	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv464150	chr1:159860917-159908393	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv548052	chr1:159860917-159908393	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv548053	chr1:159885500-159908393	Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv516637	chr1:159889686-159908393	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	62 gene(s)	inside rSNPs	diseases
8	nsv548054	chr1:159895979-159907441	Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159895600-159898200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:159895800-159898800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:159895800-159899000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:159895800-159899200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:159895800-159906600	Weak transcription	Small Intestine	intestine
6	chr1:159896000-159898800	Enhancers	Pancreas	Pancrea
7	chr1:159896000-159899000	Weak transcription	Esophagus	oesophagus
8	chr1:159896000-159899200	Weak transcription	Gastric	stomach
9	chr1:159896000-159906000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:159896200-159898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:159896200-159898800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:159896200-159899600	Weak transcription	Colonic Mucosa	Colon
13	chr1:159896200-159906000	Genic enhancers	Fetal Intestine Small	intestine
14	chr1:159896400-159899000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:159896400-159901000	Weak transcription	Fetal Thymus	thymus
16	chr1:159896400-159902200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:159896400-159906000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:159896400-159906000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:159896400-159906600	Weak transcription	Right Atrium	heart
20	chr1:159896600-159898600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:159896600-159898800	Weak transcription	Stomach Mucosa	stomach
22	chr1:159896600-159899400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:159896600-159900600	Genic enhancers	Fetal Intestine Large	intestine
24	chr1:159896600-159906000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:159896600-159906000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:159896600-159907200	Weak transcription	Fetal Heart	heart
27	chr1:159896600-159908600	Weak transcription	Fetal Kidney	kidney
28	chr1:159896800-159898800	Weak transcription	K562	blood
29	chr1:159896800-159899000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:159897000-159898400	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:159897000-159899000	Strong transcription	Fetal Stomach	stomach
32	chr1:159897000-159899800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:159897000-159902400	Strong transcription	Brain Germinal Matrix	brain
34	chr1:159897000-159906200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:159897000-159906200	Strong transcription	Fetal Brain Female	brain
36	chr1:159897200-159898200	Enhancers	GM12878-XiMat	blood
37	chr1:159897200-159898400	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:159897200-159898600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:159897200-159900800	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr1:159897200-159902400	Weak transcription	Spleen	Spleen
41	chr1:159897200-159902600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:159897400-159898200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:159897400-159898200	Enhancers	A549	lung
44	chr1:159897400-159898400	Enhancers	Fetal Muscle Leg	muscle
45	chr1:159897400-159898800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:159897400-159905400	Strong transcription	Liver	Liver
47	chr1:159897600-159898400	Enhancers	Placenta	Placenta
48	chr1:159897600-159898600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:159897600-159898600	Weak transcription	NHEK	skin
50	chr1:159897600-159898800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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