Variant report

Variant	rs6681029
Chromosome Location	chr1:150228026-150228027
allele	A/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	chr1:150227775-150228125	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr1:150227880-150228138	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr1:150227721-150228147	ECC-1	luminal epithelium:	n/a	chr1:150227926-150227945
4	MYBL2	chr1:150227681-150228532	HepG2	liver:	n/a	chr1:150227972-150227982
5	CTCF	chr1:150227736-150228680	K562	blood:	n/a	chr1:150228464-150228477 chr1:150227927-150227948 chr1:150227925-150227943 chr1:150228461-150228479 chr1:150228462-150228478 chr1:150227926-150227942
6	ZMIZ1	chr1:150227871-150228092	K562	blood:	n/a	n/a
7	ZKSCAN1	chr1:150227832-150228514	Hela-S3	cervix:	n/a	n/a
8	GATA1	chr1:150227810-150229082	K562	blood:	n/a	chr1:150228489-150228498 chr1:150228609-150228620 chr1:150228806-150228814
9	GTF2F1	chr1:150227797-150228821	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr1:150227960-150228110	HFF	foreskin:	n/a	n/a
11	CTCF	chr1:150227880-150228030	GM12871	blood:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
12	MYC	chr1:150227873-150228095	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr1:150227984-150228270	K562	blood:	n/a	chr1:150228084-150228098
14	CTCF	chr1:150227880-150228030	HUVEC	blood vessel:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
15	TAF1	chr1:150227795-150228101	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:150227920-150228070	HFF-Myc	foreskin:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
17	CTCF	chr1:150227794-150228809	HCT-116	colon:	n/a	chr1:150228464-150228477 chr1:150227927-150227948 chr1:150227925-150227943 chr1:150228461-150228479 chr1:150228462-150228478 chr1:150227926-150227942
18	BACH1	chr1:150227986-150228248	K562	blood:	n/a	n/a
19	MYC	chr1:150227843-150228066	HepG2	liver:	n/a	n/a
20	CTCF	chr1:150227743-150228170	T-47D	breast:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
21	CTCF	chr1:150227792-150228042	Fibrobl	skin:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
22	RFX5	chr1:150227784-150228942	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr1:150227716-150228117	SK-N-SH_RA	brain:	n/a	chr1:150227926-150227945
24	RAD21	chr1:150227768-150228090	GM12878	blood:	n/a	chr1:150227926-150227945
25	RCOR1	chr1:150227921-150228671	K562	blood:	n/a	n/a
26	CTCF	chr1:150227880-150228030	HVMF	connective:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
27	ZC3H11A	chr1:150227903-150228096	K562	blood:	n/a	n/a
28	CTCF	chr1:150227880-150228030	GM12869	blood:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
29	MYC	chr1:150227774-150228622	K562	blood:	n/a	n/a
30	POLR2A	chr1:150227869-150228643	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr1:150227799-150228073	Lung_OC	lung:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
32	RCOR1	chr1:150227805-150228116	GM12878	blood:	n/a	n/a
33	RAD21	chr1:150227736-150228808	MCF-7	breast:	n/a	chr1:150228462-150228481 chr1:150227926-150227945 chr1:150228463-150228477
34	CTCF	chr1:150227900-150228050	AG09319	gingival:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
35	RAD21	chr1:150227763-150228613	K562	blood:	n/a	chr1:150228462-150228481 chr1:150227926-150227945 chr1:150228463-150228477
36	CTCF	chr1:150227880-150228030	GM12873	blood:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
37	CTCF	chr1:150227713-150228174	K562	blood:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
38	TEAD4	chr1:150227733-150228735	K562	blood:	n/a	n/a
39	ELK1	chr1:150227904-150228109	K562	blood:	n/a	n/a
40	CTCF	chr1:150227900-150228050	Caco-2	colon:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
41	CTCF	chr1:150227880-150228030	MCF-7	breast:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
42	SMC3	chr1:150227569-150229282	SK-N-SH	brain:	n/a	chr1:150227927-150227941 chr1:150228463-150228477
43	REST	chr1:150227885-150229414	H1-neurons	neurons:	n/a	chr1:150228972-150228985 chr1:150229203-150229211
44	CTCF	chr1:150227795-150228042	ECC-1	luminal epithelium:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
45	CTCF	chr1:150227880-150228030	SK-N-SH_RA	brain:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
46	CTCF	chr1:150227728-150228200	HepG2	liver:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
47	CTCF	chr1:150227880-150228030	HFF-Myc	foreskin:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
48	CTCF	chr1:150227900-150228050	HA-sp	spinal cord:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
49	CTCF	chr1:150227817-150228029	A549	lung:	n/a	chr1:150227927-150227948 chr1:150227925-150227943 chr1:150227926-150227942
50	RAD21	chr1:150227660-150228804	HCT-116	colon:	n/a	chr1:150228462-150228481 chr1:150227926-150227945 chr1:150228463-150228477

No.	Distal block	Cell Line	Cell type
1	chr1:150226594..150229990-chr1:150253466..150255722,4	K562	blood:
2	chr1:150213534..150216403-chr1:150227957..150229503,2	K562	blood:
3	chr1:150205585..150209843-chr1:150227901..150231226,5	K562	blood:
4	chr1:150227836..150230192-chr1:150521467..150523893,3	MCF-7	breast:
5	chr1:150206994..150209857-chr1:150226998..150229481,3	MCF-7	breast:
6	chr1:150227526..150228300-chr1:150436799..150437466,2	K562	blood:
7	chr1:150227658..150229040-chr1:150253371..150254468,12	MCF-7	breast:
8	chr1:150226746..150229990-chr1:150252728..150255652,4	K562	blood:
9	chr1:150227457..150228673-chr1:150253378..150254274,5	K562	blood:
10	chr1:150227627..150228413-chr1:150402079..150402814,2	MCF-7	breast:
11	chr1:150227669..150229259-chr17:57915555..57917857,2	MCF-7	breast:
12	chr1:150227212..150229263-chr1:150253177..150254704,26	MCF-7	breast:
13	chr1:150226452..150228331-chr1:150575620..150577164,2	MCF-7	breast:
14	chr1:150227245..150229462-chr1:150292549..150295483,2	K562	blood:
15	chr1:150211882..150213572-chr1:150226427..150228895,2	K562	blood:
16	chr1:150227702..150230865-chr1:150236687..150241657,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APH1A-2	chr1:150227489-150228150	ENSG00000271845.1

Variant related genes	Relation type
CA14	TF binding region
ENSG00000225996	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000117362	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2298161	0.84[YRI][hapmap]
rs6688118	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs74126630	1.00[AFR][1000 genomes]
rs74126633	1.00[AFR][1000 genomes]

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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv872415	chr1:150210538-150248046	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150227600-150229200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:150227800-150228200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:150227800-150228200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:150227800-150228200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:150227800-150228200	Enhancers	Ovary	ovary
6	chr1:150227800-150228600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:150227800-150233200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:150228000-150228200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:150228000-150228200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:150228000-150228200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:150228000-150228200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:150228000-150228200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:150228000-150228200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:150228000-150228200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:150228000-150228200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:150228000-150228200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:150228000-150228200	Active TSS	Brain Angular Gyrus	brain
18	chr1:150228000-150228200	Active TSS	Brain Anterior Caudate	brain
19	chr1:150228000-150228200	Active TSS	Brain Substantia Nigra	brain
20	chr1:150228000-150228200	Enhancers	Fetal Heart	heart
21	chr1:150228000-150228200	Flanking Active TSS	Fetal Kidney	kidney
22	chr1:150228000-150228200	Active TSS	Left Ventricle	heart
23	chr1:150228000-150228200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:150228000-150228200	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:150228000-150228200	Flanking Active TSS	Thymus	Thymus
26	chr1:150228000-150228400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr1:150228000-150228400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:150228000-150228400	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr1:150228000-150228400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
30	chr1:150228000-150228400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr1:150228000-150228400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr1:150228000-150228400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:150228000-150228400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:150228000-150228400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:150228000-150228400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:150228000-150228400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:150228000-150228400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:150228000-150228400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr1:150228000-150228400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:150228000-150228400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:150228000-150228400	Flanking Active TSS	Liver	Liver
42	chr1:150228000-150228400	Active TSS	Brain Germinal Matrix	brain
43	chr1:150228000-150228400	Active TSS	Colonic Mucosa	Colon
44	chr1:150228000-150228400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr1:150228000-150228400	Active TSS	Fetal Brain Female	brain
46	chr1:150228000-150228400	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr1:150228000-150228400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
48	chr1:150228000-150228400	Active TSS	Psoas Muscle	Psoas
49	chr1:150228000-150228400	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr1:150228000-150228400	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links