Variant report

Variant	rs539356692
Chromosome Location	chr7:39606439-39606440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr7:39605480-39606525	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:39605607-39606472	HCT-116	colon:	n/a	n/a
3	MXI1	chr7:39605450-39606464	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr7:39605570-39606517	A549	lung:	n/a	n/a
5	GABPA	chr7:39605475-39606452	HL-60	blood:	n/a	n/a
6	MAX	chr7:39605363-39606686	NB4	blood:	n/a	n/a
7	MXI1	chr7:39605624-39606496	Hela-S3	cervix:	n/a	n/a
8	PML	chr7:39605304-39606460	K562	blood:	n/a	n/a
9	POLR2A	chr7:39605585-39606496	K562	blood:	n/a	n/a
10	IRF1	chr7:39605505-39606689	K562	blood:	n/a	chr7:39606649-39606660 chr7:39606649-39606663 chr7:39606648-39606662 chr7:39606651-39606665 chr7:39606647-39606661
11	HEY1	chr7:39605554-39606515	K562	blood:	n/a	n/a
12	STAT3	chr7:39606390-39606706	MCF10A-Er-Src	breast:	n/a	chr7:39606650-39606661
13	POLR2A	chr7:39605039-39606825	MCF10A-Er-Src	breast:	n/a	n/a
14	CHD2	chr7:39605448-39606546	GM12878	blood:	n/a	n/a
15	MAFK	chr7:39605716-39606465	Hela-S3	cervix:	n/a	n/a
16	RELA	chr7:39605520-39606541	GM10847	blood:	n/a	n/a
17	MAX	chr7:39605506-39606459	SK-N-SH	brain:	n/a	n/a
18	GABPA	chr7:39605516-39606573	A549	lung:	n/a	n/a
19	TAF1	chr7:39605512-39606480	ECC-1	luminal epithelium:	n/a	n/a
20	HCFC1	chr7:39605177-39606969	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr7:39605593-39606484	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr7:39605437-39606601	Hela-S3	cervix:	n/a	n/a
23	MYC	chr7:39605360-39606582	NB4	blood:	n/a	n/a
24	POLR2A	chr7:39605178-39606441	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr7:39605593-39606450	GM18505	blood:	n/a	n/a
26	GABPA	chr7:39605226-39606693	A549	lung:	n/a	n/a
27	REST	chr7:39605339-39606785	H1-neurons	neurons:	n/a	chr7:39606167-39606177
28	MAZ	chr7:39605610-39606580	IMR90	lung:	n/a	n/a
29	POLR2A	chr7:39605520-39606453	GM12892	blood:	n/a	n/a
30	SMC3	chr7:39605396-39606621	Hela-S3	cervix:	n/a	n/a
31	SMARCC1	chr7:39605505-39606592	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr7:39605175-39606534	GM12878	blood:	n/a	n/a
33	POLR2A	chr7:39605502-39606443	GM12878	blood:	n/a	n/a
34	MXI1	chr7:39605566-39606605	GM12878	blood:	n/a	n/a
35	MAX	chr7:39605456-39606470	A549	lung:	n/a	n/a
36	NR2F2	chr7:39605655-39606440	MCF-7	breast:	n/a	n/a
37	RELA	chr7:39605464-39606528	GM19099	blood:	n/a	n/a
38	MXI1	chr7:39605191-39606518	IMR90	lung:	n/a	n/a
39	GABPA	chr7:39605290-39606678	SK-N-SH	brain:	n/a	n/a
40	STAT3	chr7:39606345-39606454	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:39605563-39606614	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr7:39605345-39606755	GM12878	blood:	n/a	n/a
43	MAX	chr7:39605526-39606558	SK-N-SH	brain:	n/a	n/a
44	SIN3A	chr7:39605265-39606618	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr7:39604938-39607300	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr7:39605511-39606596	HUVEC	blood vessel:	n/a	n/a
47	CEBPB	chr7:39605220-39606506	Hela-S3	cervix:	n/a	n/a
48	SIN3AK20	chr7:39605573-39606620	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr7:39605177-39606615	PBDE	blood:	n/a	n/a
50	KAP1	chr7:39605396-39606540	HEK293	kidney:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:39604710..39608797-chr7:39663149..39665225,4	K562	blood:
2	chr7:39605618..39607861-chr7:39772706..39774759,2	K562	blood:
3	chr12:120729013..120729820-chr7:39605948..39606462,2	Hela-S3	cervix:
4	chr7:39605012..39607338-chr7:39986740..39989686,2	K562	blood:
5	chr7:39605969..39608430-chr7:39663149..39665540,3	K562	blood:
6	chr7:39606078..39608053-chr7:39609216..39613025,4	MCF-7	breast:

No data

Variant related genes	Relation type
YAE1D1	TF binding region
ENSG00000227172	TF binding region
ENSG00000006451	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000065883	Chromatin interaction
ENSG00000236015	Chromatin interaction
ENSG00000188185	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000259826	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv970467	chr7:39605971-39615006	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr7:39604600-39606600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr7:39605000-39606600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:39605000-39606600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr7:39605000-39606800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:39605000-39606800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:39605000-39606800	Active TSS	Aorta	Aorta
7	chr7:39605000-39606800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:39605000-39606800	Active TSS	GM12878-XiMat	blood
9	chr7:39605000-39606800	Active TSS	HMEC	breast
10	chr7:39605000-39606800	Active TSS	K562	blood
11	chr7:39605000-39607000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr7:39605000-39607000	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr7:39605000-39607000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr7:39605000-39607000	Active TSS	Fetal Kidney	kidney
15	chr7:39605000-39607000	Active TSS	NHDF-Ad	bronchial
16	chr7:39605000-39607200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:39605000-39607200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:39605000-39607200	Active TSS	Rectal Smooth Muscle	rectum
19	chr7:39605000-39607400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:39605000-39607600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr7:39605000-39607600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr7:39605000-39607600	Active TSS	A549	lung
23	chr7:39605000-39607600	Active TSS	NHLF	lung
24	chr7:39605200-39606600	Active TSS	Brain Cingulate Gyrus	brain
25	chr7:39605200-39606600	Active TSS	Colonic Mucosa	Colon
26	chr7:39605200-39606600	Active TSS	Colon Smooth Muscle	Colon
27	chr7:39605200-39606600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr7:39605200-39606600	Active TSS	Fetal Heart	heart
29	chr7:39605200-39606600	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr7:39605200-39606600	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr7:39605200-39606800	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr7:39605200-39606800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:39605200-39606800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:39605200-39606800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:39605200-39606800	Active TSS	Brain Hippocampus Middle	brain
36	chr7:39605200-39606800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:39605200-39606800	ZNF genes & repeats	Fetal Brain Male	brain
38	chr7:39605200-39606800	Active TSS	Fetal Muscle Leg	muscle
39	chr7:39605200-39606800	Active TSS	Fetal Stomach	stomach
40	chr7:39605200-39606800	Active TSS	Fetal Thymus	thymus
41	chr7:39605200-39606800	Active TSS	Stomach Mucosa	stomach
42	chr7:39605200-39606800	Active TSS	Thymus	Thymus
43	chr7:39605200-39607000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:39605200-39607000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:39605200-39607000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:39605200-39607000	Active TSS	Fetal Intestine Large	intestine
47	chr7:39605200-39607000	Active TSS	Fetal Intestine Small	intestine
48	chr7:39605200-39607000	Active TSS	Ovary	ovary
49	chr7:39605200-39607000	Active TSS	Right Atrium	heart
50	chr7:39605200-39607000	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links