Variant report

Variant	rs377622047
Chromosome Location	chr3:46940001-46940002
allele	-/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:46939977-46940579	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr3:46939980-46940624	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:46938433-46940961	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:46939978-46940028	PFSK-1	brain:	n/a
2	chr3:46939978-46940028	GM12892	blood:	n/a
3	chr3:46939978-46940028	NT2-D1	testis:	n/a
4	chr3:46939978-46940028	HCF	heart:	n/a
5	chr3:46939978-46940028	GM06990	blood:	n/a
6	chr3:46939978-46940028	HRCEpiC	kidney:	n/a
7	chr3:46939978-46940028	K562	blood:	n/a
8	chr3:46939978-46940028	HMEC	breast:	n/a
9	chr3:46939978-46940028	MCF-7	breast:	n/a
10	chr3:46939978-46940028	MCF10A-Er-Src	breast:	n/a
11	chr3:46939978-46940028	Caco-2	colon:	n/a
12	chr3:46939978-46940028	NB4	blood:	n/a
13	chr3:46939978-46940028	HEEpiC	esophagus:	n/a
14	chr3:46939978-46940028	GM12878	blood:	n/a
15	chr3:46939978-46940028	BE2_C	brain:	n/a
16	chr3:46939978-46940028	SKMC	muscle:	n/a
17	chr3:46939978-46940028	HIPEpiC	eye:	n/a
18	chr3:46939978-46940028	BJ	skin:	n/a
19	chr3:46939978-46940028	Hela-S3	cervix:	n/a
20	chr3:46939978-46940028	HCPEpiC	choroid plexus:	n/a
21	chr3:46939978-46940028	IMR90	lung:	fetal
22	chr3:46939978-46940028	AG10803	skin:	n/a
23	chr3:46939978-46940028	PANC-1	pancreas:	n/a
24	chr3:46939978-46940028	SK-N-MC	brain:	n/a
25	chr3:46939978-46940028	HRPEpiC	eye:	n/a
26	chr3:46939978-46940028	CMK	blood:	n/a
27	chr3:46939978-46940028	HRE	kidney:	n/a
28	chr3:46939978-46940028	AG09319	gingival:	n/a
29	chr3:46939978-46940028	SAEC	small airway:	n/a
30	chr3:46939978-46940028	HAEpiC	amniotic membrane:	n/a
31	chr3:46939978-46940028	AG04449	skin:	fetal
32	chr3:46939978-46940028	LNCaP	prostate:	n/a
33	chr3:46939978-46940028	GM19239	blood:	n/a
34	chr3:46939978-46940028	Jurkat	blood:	n/a
35	chr3:46939978-46940028	AG09309	skin:	n/a
36	chr3:46939978-46940028	RPTEC	kidney:	n/a
37	chr3:46939978-46940028	HCM	heart:	n/a
38	chr3:46939978-46940028	HNPCEpiC	eye:	n/a
39	chr3:46939978-46940028	T-47D	breast:	n/a
40	chr3:46939978-46940028	U87	brain:	n/a
41	chr3:46939978-46940028	H1-hESC	embryonic stem cell:	embryo
42	chr3:46939978-46940028	SK-N-SH_RA	brain:	n/a
43	chr3:46939978-46940028	HCT-116	colon:	n/a
44	chr3:46939978-46940028	HepG2	liver:	n/a
45	chr3:46939978-46940028	SK-N-SH	brain:	n/a
46	chr3:46939978-46940028	ProgFib	skin:	n/a
47	chr3:46939978-46940028	GM12891	blood:	n/a
48	chr3:46939978-46940028	HUVEC	blood vessel:	n/a
49	chr3:46939978-46940028	NHDF-neo	bronchial:	n/a
50	chr3:46939978-46940028	HPAEpiC	pulmonary alveolar:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46935290..46938710-chr3:46938764..46942918,5	K562	blood:
2	chr3:46929548..46935187-chr3:46936132..46940432,7	K562	blood:
3	chr3:46924894..46926955-chr3:46938452..46941314,2	K562	blood:
4	chr3:46933982..46936274-chr3:46938142..46940231,2	MCF-7	breast:
5	chr3:46939682..46941906-chr3:46942383..46946161,3	K562	blood:
6	chr3:46939682..46941423-chr3:46942383..46944944,2	K562	blood:
7	chr3:46858188..46860125-chr3:46939783..46942119,2	K562	blood:

No data

Variant related genes	Relation type
PTH1R	TF binding region
PTH1R	CpG island
ENSG00000268537	Chromatin interaction
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription 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	18 gene(s)	inside rSNPs	diseases
7	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv3357520	chr3:46939998-46942796	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46934400-46951000	Weak transcription	Psoas Muscle	Psoas
2	chr3:46934600-46949400	Weak transcription	Fetal Kidney	kidney
3	chr3:46934800-46940200	Weak transcription	HUVEC	blood vessel
4	chr3:46935400-46940400	Weak transcription	Left Ventricle	heart
5	chr3:46939400-46940600	Bivalent Enhancer	Fetal Intestine Small	intestine
6	chr3:46939400-46940800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr3:46939400-46941400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr3:46939400-46941600	Enhancers	Spleen	Spleen
9	chr3:46939600-46940200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:46939600-46940200	Bivalent Enhancer	Fetal Brain Male	brain
11	chr3:46939600-46940200	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr3:46939600-46940400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:46939600-46940600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr3:46939600-46940600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:46939600-46940800	Enhancers	Fetal Heart	heart
16	chr3:46939600-46941400	Bivalent Enhancer	Fetal Stomach	stomach
17	chr3:46939600-46941800	Enhancers	Fetal Lung	lung
18	chr3:46939600-46945000	Weak transcription	K562	blood
19	chr3:46939800-46940200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:46939800-46940200	Enhancers	Esophagus	oesophagus
21	chr3:46939800-46940200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
22	chr3:46939800-46940400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:46939800-46940400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:46939800-46940400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr3:46939800-46940400	Active TSS	Brain Cingulate Gyrus	brain
26	chr3:46939800-46940600	Flanking Active TSS	Right Ventricle	heart
27	chr3:46939800-46940800	Enhancers	Primary B cells from cord blood	blood
28	chr3:46939800-46940800	Bivalent Enhancer	Fetal Thymus	thymus
29	chr3:46939800-46940800	Enhancers	Lung	lung
30	chr3:46940000-46940200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
31	chr3:46940000-46940200	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:46940000-46940200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
33	chr3:46940000-46940200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:46940000-46940200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr3:46940000-46940200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
36	chr3:46940000-46940200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
37	chr3:46940000-46940200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr3:46940000-46940200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr3:46940000-46940200	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr3:46940000-46940200	Active TSS	HSMM	muscle
41	chr3:46940000-46940400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
42	chr3:46940000-46940400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:46940000-46940400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:46940000-46940400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
45	chr3:46940000-46940400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:46940000-46940400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:46940000-46940400	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr3:46940000-46940400	Active TSS	Brain Germinal Matrix	brain
49	chr3:46940000-46940400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:46940000-46940400	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links