Variant report

Variant	rs28730671
Chromosome Location	chr1:9777669-9777670
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	POLR2A	chr1:9776246-9779771	K562	blood:	n/a	n/a
2	MYC	chr1:9777094-9778017	HepG2	liver:	n/a	chr1:9777426-9777435 chr1:9777777-9777793
3	POLR2A	chr1:9776781-9778603	K562	blood:	n/a	n/a
4	NFIC	chr1:9777269-9778251	HepG2	liver:	n/a	n/a
5	NFYB	chr1:9777418-9778119	K562	blood:	n/a	n/a
6	ATF2	chr1:9777537-9777992	GM12878	blood:	n/a	n/a
7	SRF	chr1:9777436-9777927	K562	blood:	n/a	n/a
8	MXI1	chr1:9777373-9777941	GM12878	blood:	n/a	chr1:9777787-9777796
9	PML	chr1:9777271-9778377	K562	blood:	n/a	n/a
10	HDAC2	chr1:9777386-9778042	K562	blood:	n/a	n/a
11	CHD2	chr1:9777292-9778266	GM12878	blood:	n/a	n/a
12	HNF4A	chr1:9777297-9777940	HepG2	liver:	n/a	chr1:9777551-9777563 chr1:9777491-9777506 chr1:9777549-9777564 chr1:9777549-9777564
13	FOXA2	chr1:9777400-9777924	HepG2	liver:	n/a	n/a
14	SIN3AK20	chr1:9777591-9777993	K562	blood:	n/a	n/a
15	USF1	chr1:9777270-9778115	K562	blood:	n/a	n/a
16	TBP	chr1:9777221-9778392	K562	blood:	n/a	n/a
17	ATF3	chr1:9777418-9777965	K562	blood:	n/a	n/a
18	POLR2A	chr1:9775573-9779381	GM12878	blood:	n/a	n/a
19	EP300	chr1:9777322-9778524	K562	blood:	n/a	chr1:9777841-9777850 chr1:9778066-9778082
20	PAX5	chr1:9777562-9778122	GM12878	blood:	n/a	chr1:9777953-9777971 chr1:9777842-9777851
21	E2F4	chr1:9777031-9778010	K562	blood:	n/a	n/a
22	POLR2A	chr1:9777437-9778228	GM12891	blood:	n/a	n/a
23	TAF1	chr1:9777375-9778039	K562	blood:	n/a	n/a
24	MBD4	chr1:9777433-9778033	HepG2	liver:	n/a	n/a
25	HDAC2	chr1:9777287-9778162	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:9777440-9778188	HL-60	blood:	n/a	n/a
27	EP300	chr1:9777428-9777957	GM12878	blood:	n/a	chr1:9777841-9777850
28	SPI1	chr1:9777292-9778303	GM12878	blood:	n/a	chr1:9777838-9777851 chr1:9777841-9777850 chr1:9777760-9777767
29	CTCF	chr1:9777520-9777670	GM12868	blood:	n/a	n/a
30	ZBTB7A	chr1:9777573-9777838	HepG2	liver:	n/a	n/a
31	USF1	chr1:9777592-9777981	H1-hESC	embryonic stem cell:	n/a	n/a
32	PML	chr1:9777207-9778058	K562	blood:	n/a	n/a
33	CTCF	chr1:9777640-9777790	HL-60	blood:	n/a	n/a
34	CTCF	chr1:9777310-9777673	K562	blood:	n/a	chr1:9777504-9777517 chr1:9777502-9777520
35	GABPA	chr1:9777109-9778189	K562	blood:	n/a	n/a
36	EP300	chr1:9777509-9778066	HepG2	liver:	n/a	chr1:9777841-9777850
37	MAFK	chr1:9777445-9778281	K562	blood:	n/a	n/a
38	POLR2A	chr1:9777423-9778309	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:9777156-9778316	K562	blood:	n/a	n/a
40	POLR2A	chr1:9776174-9780433	K562	blood:	n/a	n/a
41	POLR2A	chr1:9777505-9778055	GM12892	blood:	n/a	n/a
42	HNF4A	chr1:9777275-9778005	HepG2	liver:	n/a	chr1:9777551-9777563 chr1:9777491-9777506 chr1:9777549-9777564 chr1:9777549-9777564
43	MBD4	chr1:9777365-9778128	HepG2	liver:	n/a	n/a
44	CTCF	chr1:9777600-9777750	GM12872	blood:	n/a	n/a
45	BHLHE40	chr1:9777170-9778393	K562	blood:	n/a	n/a
46	ELF1	chr1:9777187-9778165	GM12878	blood:	n/a	chr1:9777840-9777851 chr1:9777839-9777850
47	MYC	chr1:9776955-9779580	K562	blood:	n/a	chr1:9777426-9777435 chr1:9777777-9777793
48	ZBTB7A	chr1:9777023-9778369	K562	blood:	n/a	chr1:9777410-9777418
49	YY1	chr1:9777012-9778219	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:9777334-9779567	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9746655..9749475-chr1:9776621..9778385,2	K562	blood:
2	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
3	chr1:9776353..9779413-chr1:9969324..9972333,3	K562	blood:
4	chr1:9777325..9778983-chr1:9792755..9795426,2	K562	blood:

Variant related genes	Relation type
PIK3CD	TF binding region
ENSG00000171608	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000231789	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2230735	0.83[ASN][1000 genomes]
rs28730674	1.00[ASN][1000 genomes]
rs28730676	0.96[ASN][1000 genomes]
rs28730677	0.85[ASN][1000 genomes]
rs4486456	0.92[ASN][1000 genomes]
rs72633870	1.00[ASN][1000 genomes]
rs72871215	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription 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	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9751000-9779800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:9761000-9779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:9761000-9781600	Weak transcription	HSMMtube	muscle
5	chr1:9761400-9778000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:9763200-9782400	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:9766000-9778800	Weak transcription	NHDF-Ad	bronchial
8	chr1:9766000-9779000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:9766000-9779000	Weak transcription	Osteobl	bone
10	chr1:9766200-9779000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
12	chr1:9769200-9783600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:9770200-9778800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:9770800-9782600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:9771600-9782600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:9771800-9778800	Weak transcription	NH-A	brain
17	chr1:9772400-9778800	Weak transcription	HSMM	muscle
18	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:9773200-9778400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:9773400-9778800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:9774000-9778400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:9774600-9783400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:9774800-9782600	Strong transcription	Brain Germinal Matrix	brain
24	chr1:9775200-9779400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
25	chr1:9775400-9782000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:9775600-9779000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:9775600-9779000	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr1:9775600-9783400	Strong transcription	Fetal Brain Female	brain
29	chr1:9776000-9778800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:9776000-9779400	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:9776000-9779600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:9776200-9778000	Strong transcription	NHEK	skin
33	chr1:9776200-9778400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:9776200-9778400	Strong transcription	NHLF	lung
35	chr1:9776200-9780000	Genic enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:9776400-9778000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:9776400-9778800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:9776400-9780000	Enhancers	Placenta	Placenta
39	chr1:9776600-9777800	Transcr. at gene 5' and 3'	Esophagus	oesophagus
40	chr1:9776600-9778200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:9776600-9778400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:9776600-9778400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:9776600-9778600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
44	chr1:9776600-9779400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:9776600-9779800	Flanking Active TSS	K562	blood
46	chr1:9776800-9778000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:9776800-9778000	Active TSS	Duodenum Mucosa	Duodenum
48	chr1:9776800-9778600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr1:9776800-9778800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:9776800-9781800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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