Variant report

Variant	rs2973035
Chromosome Location	chr5:37838321-37838322
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	ZNF143	chr5:37838243-37838484	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr5:37838284-37838420	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr5:37838274-37838487	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr5:37838280-37838430	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr5:37838320-37838470	GM12873	blood:	n/a	n/a
6	CTCF	chr5:37838220-37838370	AG04450	lung:	n/a	n/a
7	CTCF	chr5:37838220-37838370	BE2_C	brain:	n/a	n/a
8	CTCF	chr5:37838300-37838450	HBMEC	blood vessel:	n/a	n/a
9	SIN3AK20	chr5:37838144-37838564	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr5:37838320-37838470	HUVEC	blood vessel:	n/a	n/a
11	MAX	chr5:37838109-37839800	H1-hESC	embryonic stem cell:	n/a	chr5:37839592-37839602 chr5:37839378-37839388 chr5:37839135-37839145
12	CTCF	chr5:37838318-37838495	GM19239	blood:	n/a	n/a
13	CTCF	chr5:37838320-37838470	GM12870	blood:	n/a	n/a
14	CTCF	chr5:37838300-37838450	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr5:37838280-37838430	HRPEpiC	eye:	n/a	n/a
16	CTCF	chr5:37838298-37838493	T-47D	breast:	n/a	n/a
17	E2F6	chr5:37837818-37839512	H1-hESC	embryonic stem cell:	n/a	chr5:37838340-37838347 chr5:37838955-37838964 chr5:37838113-37838121 chr5:37838400-37838407 chr5:37838739-37838747 chr5:37838340-37838347 chr5:37838739-37838747 chr5:37838112-37838122 chr5:37838663-37838672 chr5:37838113-37838120 chr5:37838340-37838347 chr5:37838113-37838121 chr5:37838112-37838123
18	CTCF	chr5:37838284-37838525	GM12878	blood:	n/a	n/a
19	CTCF	chr5:37838300-37838450	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr5:37838300-37838450	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:37836766-37838645	U87	brain:	n/a	n/a
22	CTCF	chr5:37838320-37838470	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr5:37838300-37838450	HPAF	blood vessel:	n/a	n/a
24	CTCF	chr5:37838280-37838430	HEEpiC	esophagus:	n/a	n/a
25	CTCF	chr5:37838300-37838450	MCF-7	breast:	n/a	n/a
26	CTCF	chr5:37838300-37838496	GM12891	blood:	n/a	n/a
27	CTCF	chr5:37838320-37838470	HRE	kidney:	n/a	n/a
28	RAD21	chr5:37837286-37838708	SK-N-SH	brain:	n/a	chr5:37837660-37837673 chr5:37837657-37837676 chr5:37837662-37837674 chr5:37837662-37837672 chr5:37837656-37837670
29	CTCF	chr5:37838280-37838430	GM12873	blood:	n/a	n/a
30	RCOR1	chr5:37836628-37839609	IMR90	lung:	n/a	n/a
31	CTCF	chr5:37838308-37838504	MCF-7	breast:	n/a	n/a
32	CTCF	chr5:37838300-37838450	HMF	breast:	n/a	n/a
33	RAD21	chr5:37838275-37838510	SK-N-SH_RA	brain:	n/a	n/a
34	CTCF	chr5:37836714-37838837	SK-N-SH	brain:	n/a	chr5:37837658-37837679 chr5:37838657-37838670 chr5:37837659-37837672 chr5:37838584-37838597 chr5:37837979-37837992 chr5:37837656-37837674
35	CTCF	chr5:37838320-37838470	HRPEpiC	eye:	n/a	n/a
36	CTCF	chr5:37838301-37838516	MCF-7	breast:	n/a	n/a
37	CTCF	chr5:37838320-37838470	GM12871	blood:	n/a	n/a
38	CTCF	chr5:37838310-37838505	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr5:37838320-37838470	MCF-7	breast:	n/a	n/a
40	RAD21	chr5:37838159-37838874	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr5:37836600-37838833	IMR90	lung:	n/a	chr5:37837403-37837410 chr5:37837199-37837209 chr5:37837402-37837411 chr5:37837696-37837705 chr5:37837402-37837411
42	CTCF	chr5:37838280-37838430	AoAF	blood vessel:	n/a	n/a
43	CTCF	chr5:37838260-37838410	HFF-Myc	foreskin:	n/a	n/a
44	CTCF	chr5:37838240-37838390	GM12878	blood:	n/a	n/a
45	CTCF	chr5:37838300-37838450	HMEC	breast:	n/a	n/a
46	CTCF	chr5:37838286-37838514	GM19238	blood:	n/a	n/a
47	MAX	chr5:37838186-37838636	SK-N-SH	brain:	n/a	n/a
48	CTCF	chr5:37838320-37838470	AG09319	gingival:	n/a	n/a
49	CTCF	chr5:37838240-37838390	BE2_C	brain:	n/a	n/a
50	CTCF	chr5:37838300-37838450	AG10803	skin:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:37838290-37838340	HUVEC	blood vessel:	n/a
2	chr5:37838290-37838340	IMR90	lung:	fetal
3	chr5:37838290-37838340	ProgFib	skin:	n/a
4	chr5:37838290-37838340	Caco-2	colon:	n/a
5	chr5:37838290-37838340	HEEpiC	esophagus:	n/a
6	chr5:37838290-37838340	Jurkat	blood:	n/a
7	chr5:37838290-37838340	SK-N-MC	brain:	n/a
8	chr5:37838290-37838340	Hepatocyte	liver:	n/a
9	chr5:37838290-37838340	HIPEpiC	eye:	n/a
10	chr5:37838290-37838340	NHBE	bronchial:	n/a
11	chr5:37838290-37838340	SKMC	muscle:	n/a
12	chr5:37838290-37838340	AG09309	skin:	n/a
13	chr5:37838290-37838340	GM12891	blood:	n/a
14	chr5:37838290-37838340	AoSMC	blood vessel:	n/a
15	chr5:37838290-37838340	CMK	blood:	n/a
16	chr5:37838290-37838340	SK-N-SH_RA	brain:	n/a
17	chr5:37838290-37838340	SAEC	small airway:	n/a
18	chr5:37838290-37838340	HCM	heart:	n/a
19	chr5:37838290-37838340	NT2-D1	testis:	n/a
20	chr5:37838290-37838340	Hela-S3	cervix:	n/a
21	chr5:37838290-37838340	GM19239	blood:	n/a
22	chr5:37838290-37838340	ECC-1	luminal epithelium:	n/a
23	chr5:37838290-37838340	A549	lung:	n/a
24	chr5:37838290-37838340	ovcar-3	ovarian:	n/a
25	chr5:37838290-37838340	HCPEpiC	choroid plexus:	n/a
26	chr5:37838290-37838340	GM12892	blood:	n/a
27	chr5:37838290-37838340	K562	blood:	n/a
28	chr5:37838290-37838340	PANC-1	pancreas:	n/a
29	chr5:37838290-37838340	PrEC	prostate:	n/a
30	chr5:37838290-37838340	HCF	heart:	n/a
31	chr5:37838290-37838340	BE2_C	brain:	n/a
32	chr5:37838290-37838340	LNCaP	prostate:	n/a
33	chr5:37838290-37838340	NHDF-neo	bronchial:	n/a
34	chr5:37838290-37838340	NB4	blood:	n/a
35	chr5:37838290-37838340	AG04449	skin:	fetal
36	chr5:37838290-37838340	HNPCEpiC	eye:	n/a
37	chr5:37838290-37838340	GM12878	blood:	n/a
38	chr5:37838290-37838340	MCF-7	breast:	n/a
39	chr5:37838290-37838340	AG09319	gingival:	n/a
40	chr5:37838290-37838340	AG10803	skin:	n/a
41	chr5:37838290-37838340	HPAEpiC	pulmonary alveolar:	n/a
42	chr5:37838290-37838340	HL-60	blood:	n/a
43	chr5:37838290-37838340	HAEpiC	amniotic membrane:	n/a
44	chr5:37838290-37838340	T-47D	breast:	n/a
45	chr5:37838290-37838340	HepG2	liver:	n/a
46	chr5:37838290-37838340	U87	brain:	n/a
47	chr5:37838290-37838340	AG04450	lung:	fetal
48	chr5:37838290-37838340	HRCEpiC	kidney:	n/a
49	chr5:37838290-37838340	RPTEC	kidney:	n/a
50	chr5:37838290-37838340	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:37837099..37839105-chr5:37840105..37842875,2	K562	blood:
2	chr5:37837235..37838357-chr5:38188854..38190044,6	MCF-7	breast:
3	chr5:37837605..37839454-chr5:37840945..37842875,2	K562	blood:
4	chr5:37836730..37838460-chr5:38192942..38193858,10	MCF-7	breast:

Variant related genes	Relation type
GDNF	TF binding region
GDNF-AS1	TF binding region
GDNF-AS1	CpG island
GDNF	CpG island
ENSG00000248587	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10060017	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13361833	0.86[ASN][1000 genomes]
rs1423448	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075680	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075681	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2366621	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910692	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2910694	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2910697	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2910698	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2910699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2910700	0.92[ASN][1000 genomes]
rs2910701	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2910705	0.85[ASN][1000 genomes]
rs2910706	0.85[ASN][1000 genomes]
rs2910707	0.86[ASN][1000 genomes]
rs2910749	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2910757	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910759	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910760	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910797	0.86[ASN][1000 genomes]
rs2973036	0.82[ASN][1000 genomes]
rs2973045	0.84[ASN][1000 genomes]
rs2973046	0.85[ASN][1000 genomes]
rs2973047	0.86[ASN][1000 genomes]
rs2973107	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2973112	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973117	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973118	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2973119	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973120	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973121	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973122	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2975100	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67720228	0.85[ASN][1000 genomes]
rs884344	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv1844348	chr5:37835398-37840642	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1851519	chr5:37835398-37840642	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37834200-37838400	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr5:37834200-37839000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:37834200-37841000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:37834400-37838800	Active TSS	Colon Smooth Muscle	Colon
5	chr5:37834400-37840600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr5:37834400-37841400	Bivalent/Poised TSS	Colonic Mucosa	Colon
7	chr5:37835000-37839800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
8	chr5:37835800-37840000	Bivalent Enhancer	Spleen	Spleen
9	chr5:37836000-37839400	Bivalent/Poised TSS	Fetal Kidney	kidney
10	chr5:37836200-37839000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:37836200-37840200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:37836200-37840600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr5:37836200-37840800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:37836200-37840800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr5:37836200-37840800	Active TSS	NHDF-Ad	bronchial
16	chr5:37836200-37841000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr5:37836200-37841000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:37836400-37839600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
19	chr5:37836400-37839600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
20	chr5:37836400-37839800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr5:37836400-37839800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr5:37836400-37840600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:37836400-37840600	Active TSS	HSMM	muscle
24	chr5:37836400-37840800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr5:37836400-37841200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:37836400-37841600	Active TSS	HSMMtube	muscle
27	chr5:37836600-37838400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr5:37836600-37838600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
29	chr5:37836600-37838600	Active TSS	Psoas Muscle	Psoas
30	chr5:37836600-37838800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:37836600-37838800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:37836600-37838800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
33	chr5:37836600-37839000	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:37836600-37839000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:37836600-37839400	Active TSS	Aorta	Aorta
36	chr5:37836600-37839800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr5:37836600-37839800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr5:37836600-37840000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
39	chr5:37836600-37840000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
40	chr5:37836600-37840200	Enhancers	Lung	lung
41	chr5:37836600-37841000	Flanking Active TSS	HMEC	breast
42	chr5:37836800-37838400	Active TSS	Ovary	ovary
43	chr5:37836800-37838600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr5:37836800-37838800	Flanking Bivalent TSS/Enh	Placenta	Placenta
45	chr5:37836800-37839400	Flanking Active TSS	Liver	Liver
46	chr5:37837000-37838400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
47	chr5:37837000-37838600	Bivalent Enhancer	Primary B cells from cord blood	blood
48	chr5:37837000-37839200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:37837000-37840600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr5:37837000-37840800	Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links