Variant report

Variant	rs1128306
Chromosome Location	chr6:29943269-29943270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:29942917-29943629	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr6:29942686-29943660	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr6:29943179-29943683	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr6:29942891-29943637	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:29943260-29943410	WERI-Rb-1	eye:	n/a	n/a
6	MAX	chr6:29942882-29943628	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29943268-29943318	AG09309	skin:	n/a
2	chr6:29943268-29943318	SK-N-MC	brain:	n/a
3	chr6:29943268-29943318	AG04450	lung:	fetal
4	chr6:29943268-29943318	NB4	blood:	n/a
5	chr6:29943268-29943318	HRE	kidney:	n/a
6	chr6:29943268-29943318	NHBE	bronchial:	n/a
7	chr6:29943268-29943318	HCM	heart:	n/a
8	chr6:29943268-29943318	AG09319	gingival:	n/a
9	chr6:29943268-29943318	HepG2	liver:	n/a
10	chr6:29943268-29943318	Hela-S3	cervix:	n/a
11	chr6:29943268-29943318	LNCaP	prostate:	n/a
12	chr6:29943268-29943318	ovcar-3	ovarian:	n/a
13	chr6:29943268-29943318	ECC-1	luminal epithelium:	n/a
14	chr6:29943268-29943318	GM12892	blood:	n/a
15	chr6:29943268-29943318	PrEC	prostate:	n/a
16	chr6:29943268-29943318	NH-A	brain:	n/a
17	chr6:29943268-29943318	CMK	blood:	n/a
18	chr6:29943268-29943318	Hepatocyte	liver:	n/a
19	chr6:29943268-29943318	SK-N-SH	brain:	n/a
20	chr6:29943268-29943318	T-47D	breast:	n/a
21	chr6:29943268-29943318	SKMC	muscle:	n/a
22	chr6:29943268-29943318	NHDF-neo	bronchial:	n/a
23	chr6:29943268-29943318	BE2_C	brain:	n/a
24	chr6:29943268-29943318	HUVEC	blood vessel:	n/a
25	chr6:29943268-29943318	AG04449	skin:	fetal
26	chr6:29943268-29943318	GM12891	blood:	n/a
27	chr6:29943268-29943318	HRCEpiC	kidney:	n/a
28	chr6:29943268-29943318	GM19239	blood:	n/a
29	chr6:29943268-29943318	A549	lung:	n/a
30	chr6:29943268-29943318	GM06990	blood:	n/a
31	chr6:29943268-29943318	HEEpiC	esophagus:	n/a
32	chr6:29943268-29943318	H1-hESC	embryonic stem cell:	embryo
33	chr6:29943268-29943318	SK-N-SH_RA	brain:	n/a
34	chr6:29943268-29943318	Jurkat	blood:	n/a
35	chr6:29943268-29943318	HCF	heart:	n/a
36	chr6:29943268-29943318	HCT-116	colon:	n/a
37	chr6:29943268-29943318	HNPCEpiC	eye:	n/a
38	chr6:29943268-29943318	NT2-D1	testis:	n/a
39	chr6:29943268-29943318	HRPEpiC	eye:	n/a
40	chr6:29943268-29943318	HL-60	blood:	n/a
41	chr6:29943268-29943318	ProgFib	skin:	n/a
42	chr6:29943268-29943318	U87	brain:	n/a
43	chr6:29943268-29943318	BJ	skin:	n/a
44	chr6:29943268-29943318	HEK293	kidney:	embryo
45	chr6:29943268-29943318	GM12878	blood:	n/a
46	chr6:29943268-29943318	HAEpiC	amniotic membrane:	n/a
47	chr6:29943268-29943318	HPAEpiC	pulmonary alveolar:	n/a
48	chr6:29943268-29943318	PFSK-1	brain:	n/a
49	chr6:29943268-29943318	MCF10A-Er-Src	breast:	n/a
50	chr6:29943268-29943318	HCPEpiC	choroid plexus:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29943013..29944901-chr6:29959011..29961264,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLA-A-1	chr6:29942889-29943294	ENSG00000204625
2	lnc-HLA-A-1	chr6:29942892-29943294	NR_028032

No data

Variant related genes	Relation type
HCG9	TF binding region
MICD	TF binding region
HCG9	CpG island
MICD	CpG island
ENSG00000238024	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17180241	0.93[ASN][1000 genomes]
rs2232238	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256820	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256902	0.93[ASN][1000 genomes]
rs2517673	0.88[ASN][1000 genomes]
rs2517676	0.80[ASN][1000 genomes]
rs2523943	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2523947	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523961	0.93[ASN][1000 genomes]
rs2523967	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523969	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs400488	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422640	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453375	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv32544	chr6:29831716-29944103	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
17	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv984584	chr6:29932342-29943951	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
23	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
24	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	esv3350882	chr6:29942373-29945471	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr6:29934400-29944200	Weak transcription	Aorta	Aorta
2	chr6:29935400-29943400	Weak transcription	Small Intestine	intestine
3	chr6:29935600-29944800	Weak transcription	Dnd41	blood
4	chr6:29941600-29944400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:29942200-29943400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
6	chr6:29942200-29943400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
7	chr6:29942400-29943600	Bivalent Enhancer	Stomach Mucosa	stomach
8	chr6:29942400-29943600	Flanking Active TSS	Spleen	Spleen
9	chr6:29942600-29943400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr6:29942600-29943600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr6:29942600-29943600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:29942600-29944200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
13	chr6:29942600-29944400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr6:29942600-29944400	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:29942600-29944400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
16	chr6:29942600-29945200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:29942600-29945400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:29942600-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:29942800-29943400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:29942800-29943400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:29942800-29943400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr6:29942800-29943400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:29942800-29943400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:29942800-29943400	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr6:29942800-29943400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:29942800-29943600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:29942800-29943600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr6:29942800-29943600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:29942800-29943600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
30	chr6:29942800-29943600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
31	chr6:29942800-29943600	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr6:29942800-29943600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr6:29942800-29943600	Flanking Active TSS	Left Ventricle	heart
34	chr6:29942800-29943600	Flanking Active TSS	Pancreas	Pancrea
35	chr6:29942800-29943600	Flanking Active TSS	Right Ventricle	heart
36	chr6:29942800-29943600	Active TSS	HSMMtube	muscle
37	chr6:29942800-29943800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
38	chr6:29942800-29943800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:29942800-29943800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:29942800-29943800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
41	chr6:29942800-29944000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:29942800-29944200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr6:29942800-29944200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr6:29942800-29944400	Bivalent Enhancer	Fetal Thymus	thymus
45	chr6:29942800-29944400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr6:29942800-29944400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr6:29942800-29945400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr6:29943000-29943400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:29943000-29943400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:29943000-29943400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links