Variant report

Variant	rs28359990
Chromosome Location	chr6:29601560-29601561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr6:29599102-29601690	HEK293-T-REx	kidney:	n/a	chr6:29600781-29600802
2	TAF1	chr6:29600039-29601736	H1-neurons	neurons:	n/a	n/a
3	REST	chr6:29599777-29602043	H1-neurons	neurons:	n/a	chr6:29601089-29601102
4	POLR2A	chr6:29598104-29601707	K562	blood:	n/a	n/a
5	POLR2A	chr6:29600862-29601581	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:29599663-29601899	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr6:29599885-29601775	H1-neurons	neurons:	n/a	n/a
8	MAZ	chr6:29598835-29601887	K562	blood:	n/a	chr6:29600301-29600311 chr6:29601521-29601531
9	JUND	chr6:29600153-29601852	K562	blood:	n/a	n/a
10	POLR2A	chr6:29599054-29601572	K562	blood:	n/a	n/a
11	MAZ	chr6:29599759-29601808	IMR90	lung:	n/a	chr6:29600301-29600311 chr6:29601521-29601531
12	TBL1XR1	chr6:29601245-29601728	K562	blood:	n/a	n/a
13	SIN3A	chr6:29599830-29601885	H1-hESC	embryonic stem cell:	n/a	chr6:29601213-29601222
14	POLR2A	chr6:29599810-29601940	H1-neurons	neurons:	n/a	n/a
15	REST	chr6:29600622-29601592	H1-neurons	neurons:	n/a	chr6:29601089-29601102
16	POLR2A	chr6:29598886-29601567	K562	blood:	n/a	n/a
17	IRF1	chr6:29600778-29601601	K562	blood:	n/a	chr6:29601019-29601033
18	POLR2A	chr6:29601537-29601589	ProgFib	skin:	n/a	n/a
19	TAF1	chr6:29600756-29601629	H1-neurons	neurons:	n/a	n/a
20	RCOR1	chr6:29598543-29601805	K562	blood:	n/a	n/a
21	MYC	chr6:29599017-29601618	K562	blood:	n/a	chr6:29600301-29600311 chr6:29601521-29601531

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29601556-29601606	AG10803	skin:	n/a
2	chr6:29601556-29601606	K562	blood:	n/a
3	chr6:29601556-29601606	H1-hESC	embryonic stem cell:	embryo
4	chr6:29601556-29601606	IMR90	lung:	fetal
5	chr6:29601556-29601606	HepG2	liver:	n/a
6	chr6:29601556-29601606	ProgFib	skin:	n/a
7	chr6:29601556-29601606	T-47D	breast:	n/a
8	chr6:29601556-29601606	AG04449	skin:	fetal
9	chr6:29601556-29601606	SKMC	muscle:	n/a
10	chr6:29601556-29601606	CMK	blood:	n/a
11	chr6:29601556-29601606	NH-A	brain:	n/a
12	chr6:29601556-29601606	HAEpiC	amniotic membrane:	n/a
13	chr6:29601556-29601606	AG09309	skin:	n/a
14	chr6:29601556-29601606	SK-N-MC	brain:	n/a
15	chr6:29601556-29601606	PANC-1	pancreas:	n/a
16	chr6:29601556-29601606	LNCaP	prostate:	n/a
17	chr6:29601556-29601606	ECC-1	luminal epithelium:	n/a
18	chr6:29601556-29601606	GM12878	blood:	n/a
19	chr6:29601556-29601606	Hela-S3	cervix:	n/a
20	chr6:29601556-29601606	BJ	skin:	n/a
21	chr6:29601556-29601606	SK-N-SH	brain:	n/a
22	chr6:29601556-29601606	RPTEC	kidney:	n/a
23	chr6:29601556-29601606	HL-60	blood:	n/a
24	chr6:29601556-29601606	A549	lung:	n/a
25	chr6:29601556-29601606	PFSK-1	brain:	n/a
26	chr6:29601556-29601606	Caco-2	colon:	n/a
27	chr6:29601556-29601606	HCT-116	colon:	n/a
28	chr6:29601556-29601606	SAEC	small airway:	n/a
29	chr6:29601556-29601606	Jurkat	blood:	n/a
30	chr6:29601556-29601606	U87	brain:	n/a
31	chr6:29601556-29601606	HNPCEpiC	eye:	n/a
32	chr6:29601556-29601606	MCF-7	breast:	n/a
33	chr6:29601556-29601606	GM06990	blood:	n/a
34	chr6:29601556-29601606	HMEC	breast:	n/a
35	chr6:29601556-29601606	GM12891	blood:	n/a
36	chr6:29601556-29601606	NB4	blood:	n/a
37	chr6:29601556-29601606	AoSMC	blood vessel:	n/a
38	chr6:29601556-29601606	AG09319	gingival:	n/a
39	chr6:29601556-29601606	HRPEpiC	eye:	n/a
40	chr6:29601556-29601606	HIPEpiC	eye:	n/a
41	chr6:29601556-29601606	SK-N-SH_RA	brain:	n/a
42	chr6:29601556-29601606	MCF10A-Er-Src	breast:	n/a
43	chr6:29601556-29601606	HRE	kidney:	n/a
44	chr6:29601556-29601606	ovcar-3	ovarian:	n/a
45	chr6:29601556-29601606	NT2-D1	testis:	n/a
46	chr6:29601556-29601606	HEK293	kidney:	embryo
47	chr6:29601556-29601606	AG04450	lung:	fetal
48	chr6:29601556-29601606	NHBE	bronchial:	n/a
49	chr6:29601556-29601606	HPAEpiC	pulmonary alveolar:	n/a
50	chr6:29601556-29601606	HEEpiC	esophagus:	n/a

No data

Variant related genes	Relation type
GABBR1	TF binding region
GABBR1	CpG island

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17184388	0.89[ASN][1000 genomes]
rs17218739	0.89[ASN][1000 genomes]
rs2076482	0.81[ASN][1000 genomes]
rs2267634	0.89[ASN][1000 genomes]
rs28359962	0.81[EUR][1000 genomes]
rs28359968	0.81[EUR][1000 genomes]
rs28359991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55650674	0.89[ASN][1000 genomes]
rs55662018	0.89[ASN][1000 genomes]
rs56381026	0.89[ASN][1000 genomes]
rs61744969	0.89[ASN][1000 genomes]
rs61997184	0.89[ASN][1000 genomes]
rs740884	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258000	0.81[ASN][1000 genomes]
rs9258033	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29597600-29602200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:29598200-29602000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:29598800-29601600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:29599000-29601800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:29599000-29601800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:29599000-29602400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:29599200-29601800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:29599600-29601600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:29599600-29601600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:29599600-29601600	Active TSS	Aorta	Aorta
11	chr6:29599600-29601800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:29599600-29601800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:29599600-29601800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:29599600-29601800	Active TSS	NHLF	lung
15	chr6:29599800-29601800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:29599800-29601800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr6:29599800-29602600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:29600000-29601600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:29600000-29601600	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:29600000-29601600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:29600000-29601600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr6:29600000-29601600	Active TSS	HSMM	muscle
23	chr6:29600000-29601800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:29600000-29601800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr6:29600000-29601800	Active TSS	Colon Smooth Muscle	Colon
26	chr6:29600000-29601800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:29600000-29601800	Active TSS	Fetal Kidney	kidney
28	chr6:29600000-29601800	Active TSS	Rectal Smooth Muscle	rectum
29	chr6:29600000-29601800	Active TSS	NHDF-Ad	bronchial
30	chr6:29600000-29602000	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:29600000-29602000	Active TSS	Brain Angular Gyrus	brain
32	chr6:29600000-29602200	Active TSS	Fetal Brain Female	brain
33	chr6:29600200-29601600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:29600200-29601600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:29600200-29601600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:29600200-29601600	Active TSS	Brain Cingulate Gyrus	brain
37	chr6:29600200-29601600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
38	chr6:29600200-29601600	Active TSS	Left Ventricle	heart
39	chr6:29600200-29601600	Active TSS	Ovary	ovary
40	chr6:29600200-29601600	Active TSS	Psoas Muscle	Psoas
41	chr6:29600200-29601600	Active TSS	Right Ventricle	heart
42	chr6:29600200-29601600	Active TSS	Stomach Mucosa	stomach
43	chr6:29600200-29601600	Active TSS	HMEC	breast
44	chr6:29600200-29601600	Active TSS	HUVEC	blood vessel
45	chr6:29600200-29601800	Active TSS	Esophagus	oesophagus
46	chr6:29600200-29601800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
47	chr6:29600200-29601800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr6:29600200-29602000	Active TSS	Stomach Smooth Muscle	stomach
49	chr6:29600400-29601600	Active TSS	Duodenum Mucosa	Duodenum
50	chr6:29600400-29601800	Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links