Variant report

Variant	rs728727
Chromosome Location	chr1:228643447-228643448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELK1	chr1:228643322-228644577	K562	blood:	n/a	n/a
2	SMC3	chr1:228643268-228643768	K562	blood:	n/a	n/a
3	RAD21	chr1:228643394-228643843	MCF-7	breast:	n/a	chr1:228643629-228643642
4	CTCF	chr1:228643440-228643590	HCM	heart:	n/a	n/a
5	RAD21	chr1:228642844-228643935	SK-N-SH	brain:	n/a	chr1:228643629-228643642
6	CTCF	chr1:228643017-228643805	SK-N-SH	brain:	n/a	n/a
7	ZNF143	chr1:228643280-228643685	K562	blood:	n/a	n/a
8	MYC	chr1:228643369-228643808	K562	blood:	n/a	n/a
9	CTCF	chr1:228643440-228643590	HEEpiC	esophagus:	n/a	n/a
10	RAD21	chr1:228643396-228643783	SK-N-SH_RA	brain:	n/a	chr1:228643629-228643642
11	SMC3	chr1:228643431-228643756	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr1:228643395-228643789	K562	blood:	n/a	n/a
13	CUX1	chr1:228643174-228643765	K562	blood:	n/a	n/a
14	RAD21	chr1:228643426-228643778	IMR90	lung:	n/a	chr1:228643629-228643642
15	CTCF	chr1:228643267-228643949	HCT-116	colon:	n/a	n/a
16	ZNF274	chr1:228643104-228644282	K562	blood:	n/a	n/a
17	CTCF	chr1:228643349-228643822	K562	blood:	n/a	n/a
18	MAFF	chr1:228643305-228643827	K562	blood:	n/a	n/a
19	MXI1	chr1:228643446-228645971	K562	blood:	n/a	n/a
20	HEY1	chr1:228642729-228643813	K562	blood:	n/a	n/a
21	RAD21	chr1:228643286-228643837	MCF-7	breast:	n/a	chr1:228643629-228643642
22	CTCF	chr1:228643443-228643766	GM12878	blood:	n/a	n/a
23	CTCF	chr1:228643400-228643550	HMEC	breast:	n/a	n/a
24	POLR2A	chr1:228639970-228646628	K562	blood:	n/a	n/a
25	POLR2A	chr1:228639400-228643883	K562	blood:	n/a	n/a
26	CTCF	chr1:228643440-228643590	GM12872	blood:	n/a	n/a
27	CTCF	chr1:228643400-228643550	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr1:228643409-228643777	Hela-S3	cervix:	n/a	chr1:228643629-228643642
29	RAD21	chr1:228643410-228643721	SK-N-SH_RA	brain:	n/a	chr1:228643629-228643642
30	MAZ	chr1:228643280-228643704	K562	blood:	n/a	n/a
31	CTCF	chr1:228643440-228643590	HepG2	liver:	n/a	n/a
32	CTCF	chr1:228643440-228643590	AG09309	skin:	n/a	n/a
33	BACH1	chr1:228643179-228643796	K562	blood:	n/a	n/a
34	CTCF	chr1:228643393-228643763	IMR90	lung:	n/a	n/a
35	CTCF	chr1:228643440-228643590	HAc	cerebellar:	n/a	n/a
36	MAFK	chr1:228643358-228643621	K562	blood:	n/a	n/a
37	POLR2A	chr1:228642791-228644400	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr1:228643420-228643570	GM12864	blood:	n/a	n/a
39	MXI1	chr1:228642891-228647849	SK-N-SH	brain:	n/a	n/a
40	ARID3A	chr1:228643130-228643957	K562	blood:	n/a	n/a
41	TBL1XR1	chr1:228643245-228643934	K562	blood:	n/a	n/a
42	POLR2A	chr1:228643224-228647569	PBDE	blood:	n/a	n/a
43	BCLAF1	chr1:228642976-228646006	K562	blood:	n/a	n/a
44	POLR2A	chr1:228643050-228643798	K562	blood:	n/a	n/a
45	CTCF	chr1:228643405-228643740	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:
2	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
3	chr1:228589639..228603795-chr1:228638211..228648676,43	MCF-7	breast:
4	chr1:228356236..228360236-chr1:228642827..228646319,4	K562	blood:
5	chr1:228635196..228636992-chr1:228643144..228645156,2	MCF-7	breast:
6	chr1:228527319..228529174-chr1:228643388..228645419,2	K562	blood:
7	chr1:228598492..228599485-chr1:228643349..228644003,3	MCF-7	breast:
8	chr1:228576966..228583255-chr1:228642395..228646960,7	MCF-7	breast:
9	chr1:228629848..228632081-chr1:228641803..228644733,3	MCF-7	breast:
10	chr1:228585219..228604537-chr1:228641966..228650471,45	MCF-7	breast:
11	chr1:228643338..228644128-chr3:64246210..64246800,2	MCF-7	breast:
12	chr1:228352277..228353871-chr1:228640997..228643857,2	K562	blood:
13	chr1:228487421..228490284-chr1:228642945..228645518,2	K562	blood:
14	chr1:228572036..228574709-chr1:228642846..228645272,2	K562	blood:
15	chr1:228352175..228354992-chr1:228642370..228645679,3	K562	blood:
16	chr1:228110564..228113344-chr1:228642639..228644578,2	K562	blood:
17	chr1:228295701..228298276-chr1:228642852..228645061,2	K562	blood:
18	chr1:228357413..228360288-chr1:228642904..228645646,2	K562	blood:
19	chr1:228462628..228466791-chr1:228639657..228643732,4	K562	blood:
20	chr1:228272480..228275319-chr1:228642509..228645344,2	K562	blood:
21	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:

No data

Variant related genes	Relation type
HIST3H2BB	TF binding region
ENSG00000270104	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000270094	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000162931	Chromatin interaction
ENSG00000215811	Chromatin interaction
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10733022	0.84[JPT][hapmap]
rs10753447	0.84[CEU][hapmap]
rs10799476	0.97[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs728727	C1orf96	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228634200-228644800	Weak transcription	Gastric	stomach
2	chr1:228634400-228644200	Weak transcription	Brain Anterior Caudate	brain
3	chr1:228634400-228644600	Weak transcription	Right Atrium	heart
4	chr1:228634400-228644600	Weak transcription	Right Ventricle	heart
5	chr1:228635200-228644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228638400-228644600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:228638800-228644600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:228640000-228644000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:228640200-228644200	Weak transcription	Fetal Kidney	kidney
10	chr1:228640400-228644800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:228640600-228644200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:228640600-228644800	Weak transcription	Esophagus	oesophagus
13	chr1:228640800-228643600	Weak transcription	NHLF	lung
14	chr1:228641000-228644600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:228641000-228644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:228641800-228643600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:228641800-228644800	Weak transcription	Spleen	Spleen
18	chr1:228642200-228643600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:228642200-228644400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:228642200-228644800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:228642400-228643600	Weak transcription	NHEK	skin
22	chr1:228642400-228644200	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:228642800-228643600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:228642800-228643600	Enhancers	Fetal Intestine Small	intestine
25	chr1:228642800-228644600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr1:228643000-228643600	Weak transcription	Fetal Stomach	stomach
27	chr1:228643000-228643600	Transcr. at gene 5' and 3'	K562	blood
28	chr1:228643000-228643800	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr1:228643000-228644000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:228643000-228644200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:228643000-228644400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:228643000-228644400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:228643000-228644400	Flanking Active TSS	Fetal Brain Female	brain
34	chr1:228643000-228644600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:228643000-228647800	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:228643000-228648200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr1:228643200-228643800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:228643200-228643800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:228643200-228643800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:228643200-228644000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:228643200-228644000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr1:228643200-228644200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:228643200-228644200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:228643200-228644600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:228643200-228644600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:228643200-228647600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:228643200-228647600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:228643200-228647800	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:228643200-228647800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:228643200-228647800	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links