Variant report

Variant	rs34244251
Chromosome Location	chr1:93297180-93297181
allele	A/G
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	MYC	chr1:93297090-93298480	K562	blood:	n/a	n/a
2	POLR2A	chr1:93297047-93298626	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF143	chr1:93297034-93297948	Hela-S3	cervix:	n/a	n/a
4	EP300	chr1:93297150-93298201	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr1:93297134-93298494	HCT-116	colon:	n/a	n/a
6	TBP	chr1:93297173-93298484	K562	blood:	n/a	n/a
7	CTCF	chr1:93297060-93297210	AG04449	skin:	n/a	n/a
8	RCOR1	chr1:93297004-93298005	K562	blood:	n/a	n/a
9	CTCF	chr1:93297040-93297190	GM06990	blood:	n/a	n/a
10	SP4	chr1:93297138-93298094	H1-hESC	embryonic stem cell:	n/a	chr1:93297489-93297505 chr1:93297493-93297504
11	TAF1	chr1:93297142-93298389	ECC-1	luminal epithelium:	n/a	n/a
12	CREB1	chr1:93297179-93298267	HepG2	liver:	n/a	n/a
13	SMC3	chr1:93297132-93298037	Hela-S3	cervix:	n/a	chr1:93297764-93297774 chr1:93297491-93297501 chr1:93297487-93297501
14	CREB1	chr1:93297158-93298293	K562	blood:	n/a	n/a
15	MYBL2	chr1:93297165-93298039	HepG2	liver:	n/a	n/a
16	PML	chr1:93297172-93298738	GM12878	blood:	n/a	chr1:93297231-93297239
17	ZNF263	chr1:93296958-93298483	HEK293-T-REx	kidney:	n/a	n/a
18	CTCF	chr1:93297120-93297270	GM12869	blood:	n/a	n/a
19	MXI1	chr1:93296930-93298928	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr1:93297040-93297190	GM12873	blood:	n/a	n/a
21	CTCF	chr1:93297107-93298279	A549	lung:	n/a	chr1:93297485-93297503 chr1:93297486-93297502 chr1:93297488-93297501 chr1:93297481-93297494 chr1:93297490-93297500 chr1:93297488-93297497 chr1:93297487-93297508
22	JUN	chr1:93296739-93298602	K562	blood:	n/a	n/a
23	HCFC1	chr1:93296841-93298413	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:93297065-93298736	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:93297071-93298662	K562	blood:	n/a	n/a
26	MXI1	chr1:93297043-93298573	HepG2	liver:	n/a	n/a
27	HEY1	chr1:93297127-93298467	HepG2	liver:	n/a	n/a
28	CTCF	chr1:93297120-93297270	AG10803	skin:	n/a	n/a
29	CTCF	chr1:93296902-93298631	SK-N-SH	brain:	n/a	chr1:93297485-93297503 chr1:93297486-93297502 chr1:93297488-93297501 chr1:93297481-93297494 chr1:93297490-93297500 chr1:93297488-93297497 chr1:93297487-93297508
30	POLR2A	chr1:93297130-93298691	GM12892	blood:	n/a	n/a
31	KAP1	chr1:93297031-93298093	HEK293	kidney:	n/a	chr1:93297231-93297239
32	REST	chr1:93297070-93298708	H1-neurons	neurons:	n/a	n/a
33	CTCF	chr1:93297080-93297230	GM12865	blood:	n/a	n/a
34	FOXM1	chr1:93297172-93298468	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:93297174-93298862	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr1:93297060-93297210	HMEC	breast:	n/a	n/a
37	MAX	chr1:93297111-93298310	HCT-116	colon:	n/a	n/a
38	CTCF	chr1:93297040-93297190	SAEC	small airway:	n/a	n/a
39	CTCF	chr1:93297120-93297270	AG04450	lung:	n/a	n/a
40	POLR2A	chr1:93297090-93298430	HUVEC	blood vessel:	n/a	n/a
41	MAZ	chr1:93297060-93298172	K562	blood:	n/a	n/a
42	POLR2A	chr1:93297107-93299950	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93248724..93252766-chr1:93297083..93300077,5	MCF-7	breast:
2	chr1:93220670..93222907-chr1:93296640..93299176,3	MCF-7	breast:
3	chr1:93296297..93299381-chr1:93425183..93428047,4	K562	blood:
4	chr1:93297145..93297697-chr21:34143917..34144494,2	Hela-S3	cervix:
5	chr1:93297134..93298053-chr1:213188509..213189760,3	NB4	blood:
6	chr1:93297145..93297889-chr5:177019241..177019876,2	HCT-116	colon:
7	chr1:93249660..93252667-chr1:93296431..93299077,5	K562	blood:
8	chr1:93256019..93258677-chr1:93296885..93300584,5	K562	blood:
9	chr1:93296271..93298475-chr1:93543770..93546056,2	MCF-7	breast:
10	chr1:93296356..93298770-chr1:93426282..93429088,3	MCF-7	breast:
11	chr1:93249360..93255989-chr1:93295958..93302033,8	K562	blood:
12	chr1:93256221..93258760-chr1:93295783..93299962,5	K562	blood:
13	chr1:93297138..93298008-chr8:91657918..91658510,2	Hela-S3	cervix:
14	chr1:92764074..92765656-chr1:93296705..93299037,2	K562	blood:
15	chr1:92762794..92765730-chr1:93295925..93298205,3	K562	blood:
16	chr1:93296076..93299049-chr1:93541677..93546567,5	K562	blood:
17	chr1:93296314..93299115-chr1:93644282..93648010,4	K562	blood:
18	chr1:93296486..93299108-chr1:93543311..93545320,3	K562	blood:

Variant related genes	Relation type
RPL5	TF binding region
ENSG00000180694	Chromatin interaction
ENSG00000154511	Chromatin interaction
ENSG00000184840	Chromatin interaction
ENSG00000174842	Chromatin interaction
ENSG00000223896	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000205930	Chromatin interaction
ENSG00000067208	Chromatin interaction
ENSG00000159086	Chromatin interaction
ENSG00000117500	Chromatin interaction
ENSG00000174606	Chromatin interaction
ENSG00000122484	Chromatin interaction
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10874745	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164803	1.00[CHB][hapmap]
rs11164814	1.00[CHB][hapmap]
rs11164820	1.00[CHB][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs11164825	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164857	1.00[CHB][hapmap]
rs11577426	1.00[CHB][hapmap]
rs11578004	1.00[CHB][hapmap]
rs11578098	1.00[CHB][hapmap]
rs11582791	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586570	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800409	1.00[CHB][hapmap]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs11803097	1.00[CHB][hapmap]
rs11810217	1.00[CHB][hapmap]
rs12062315	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082659	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738654	0.82[EUR][1000 genomes]
rs12743005	1.00[CHB][hapmap]
rs12746893	1.00[CHB][hapmap]
rs12746956	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749786	1.00[CHB][hapmap]
rs12750269	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17381426	1.00[CHB][hapmap]
rs1854797	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2893226	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34041593	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34098754	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34168045	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34202284	1.00[CHB][hapmap]
rs35031391	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604026	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687931	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652510	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521417	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554594	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34244251	FAM69A	cis	Artery Tibial	GTEx
rs34244251	FAM69A	cis	parietal	SCAN
rs34244251	HFM1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93289800-93297400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:93296400-93297400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:93296600-93298000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:93296600-93298600	Bivalent/Poised TSS	HepG2	liver
5	chr1:93296800-93297200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:93296800-93297200	Enhancers	A549	lung
7	chr1:93296800-93298200	Active TSS	K562	blood
8	chr1:93297000-93297200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:93297000-93297200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:93297000-93297200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:93297000-93297200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:93297000-93297200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:93297000-93297200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:93297000-93297200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr1:93297000-93297200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:93297000-93297200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:93297000-93297200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:93297000-93297200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr1:93297000-93297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:93297000-93297200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:93297000-93297200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:93297000-93297200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:93297000-93297200	Enhancers	Brain Anterior Caudate	brain
24	chr1:93297000-93297200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr1:93297000-93297200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:93297000-93297200	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:93297000-93297200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr1:93297000-93297200	Enhancers	Fetal Muscle Leg	muscle
29	chr1:93297000-93297200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr1:93297000-93297200	Enhancers	Stomach Smooth Muscle	stomach
31	chr1:93297000-93297200	Enhancers	Thymus	Thymus
32	chr1:93297000-93297200	Enhancers	GM12878-XiMat	blood
33	chr1:93297000-93297200	Enhancers	HMEC	breast
34	chr1:93297000-93297200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr1:93297000-93297200	Enhancers	NHEK	skin
36	chr1:93297000-93297400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:93297000-93297400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:93297000-93297400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:93297000-93297400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:93297000-93297400	Enhancers	Primary B cells from peripheral blood	blood
41	chr1:93297000-93297400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:93297000-93297400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr1:93297000-93297400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:93297000-93297400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:93297000-93297400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr1:93297000-93297400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:93297000-93297400	Enhancers	Liver	Liver
48	chr1:93297000-93297400	Enhancers	Brain Angular Gyrus	brain
49	chr1:93297000-93297400	Enhancers	Esophagus	oesophagus
50	chr1:93297000-93297400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links