Variant report

Variant	rs805290
Chromosome Location	chr6:31648403-31648404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr6:31648403-31648844	GM12892	blood:	n/a	chr6:31648661-31648673
2	RAD21	chr6:31648258-31649419	MCF-7	breast:	n/a	n/a
3	RAD21	chr6:31648317-31649467	ECC-1	luminal epithelium:	n/a	n/a
4	PML	chr6:31648362-31649042	GM12878	blood:	n/a	n/a
5	MTA3	chr6:31648278-31649496	GM12878	blood:	n/a	n/a
6	MAX	chr6:31648352-31648914	K562	blood:	n/a	n/a
7	SIN3AK20	chr6:31648391-31648794	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr6:31648133-31649530	HCT-116	colon:	n/a	n/a
9	RAD21	chr6:31648380-31648941	ECC-1	luminal epithelium:	n/a	n/a
10	TBL1XR1	chr6:31648362-31648849	K562	blood:	n/a	n/a
11	RAD21	chr6:31648356-31648902	HepG2	liver:	n/a	n/a
12	CTCF	chr6:31648260-31648410	GM12874	blood:	n/a	n/a
13	CTCF	chr6:31648080-31649571	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr6:31648201-31649562	HCT-116	colon:	n/a	n/a
15	POLR2A	chr6:31648376-31648852	IMR90	lung:	n/a	n/a
16	FOXM1	chr6:31648389-31649243	GM12878	blood:	n/a	n/a
17	CTCF	chr6:31648364-31648988	K562	blood:	n/a	n/a
18	POLR2A	chr6:31647991-31648641	HepG2	liver:	n/a	n/a
19	ELF1	chr6:31648389-31648891	GM12878	blood:	n/a	chr6:31648696-31648709
20	ZMIZ1	chr6:31648390-31648806	K562	blood:	n/a	n/a
21	CTCF	chr6:31648352-31649167	HCT-116	colon:	n/a	n/a
22	MXI1	chr6:31648294-31649539	SK-N-SH	brain:	n/a	n/a
23	ZNF143	chr6:31648347-31648855	K562	blood:	n/a	n/a
24	CHD1	chr6:31647990-31649517	IMR90	lung:	n/a	n/a
25	RAD21	chr6:31648332-31648962	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr6:31648258-31649542	HCT-116	colon:	n/a	n/a
27	CTCF	chr6:31648360-31648510	HFF-Myc	foreskin:	n/a	n/a
28	MAFK	chr6:31648377-31648846	K562	blood:	n/a	n/a
29	CTCF	chr6:31648365-31648824	MCF-7	breast:	n/a	n/a
30	TEAD4	chr6:31648217-31649161	K562	blood:	n/a	n/a
31	YY1	chr6:31648382-31648822	GM12878	blood:	n/a	chr6:31648661-31648673
32	YY1	chr6:31648395-31648876	SK-N-SH_RA	brain:	n/a	chr6:31648661-31648673
33	POLR2A	chr6:31648208-31649410	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:31648359-31648479	HUVEC	blood vessel:	n/a	n/a
35	RCOR1	chr6:31648305-31649067	K562	blood:	n/a	n/a
36	MYBL2	chr6:31648378-31648954	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:31648397-31649385	Hela-S3	cervix:	n/a	n/a
38	SMC3	chr6:31648395-31649498	Hela-S3	cervix:	n/a	n/a
39	MXI1	chr6:31648401-31648889	Hela-S3	cervix:	n/a	n/a
40	ZNF263	chr6:31648352-31649189	HEK293-T-REx	kidney:	n/a	n/a
41	ZC3H11A	chr6:31648326-31648871	K562	blood:	n/a	n/a
42	YY1	chr6:31648355-31648851	K562	blood:	n/a	chr6:31648661-31648673
43	SMC3	chr6:31648252-31649407	SK-N-SH	brain:	n/a	n/a
44	FOXM1	chr6:31648387-31648903	GM12878	blood:	n/a	n/a
45	USF2	chr6:31648382-31648911	Hela-S3	cervix:	n/a	chr6:31648828-31648839
46	MXI1	chr6:31648224-31649824	IMR90	lung:	n/a	n/a
47	RUNX3	chr6:31648356-31649442	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:31648357-31649548	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr6:31648236-31649622	HUVEC	blood vessel:	n/a	n/a
50	ELF1	chr6:31648401-31649389	MCF-7	breast:	n/a	chr6:31648696-31648709 chr6:31649304-31649316

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31646949..31648911-chr6:31695355..31697312,2	MCF-7	breast:
2	chr6:31648223..31648743-chr6:31797705..31798338,2	K562	blood:
3	chr5:38555853..38556803-chr6:31648295..31649045,2	Hela-S3	cervix:
4	chr6:31647614..31649375-chr6:31762314..31763878,2	MCF-7	breast:
5	chr6:31647431..31650863-chr6:31697294..31699656,3	MCF-7	breast:
6	chr6:31599461..31602010-chr6:31647062..31649518,2	MCF-7	breast:
7	chr6:31647104..31649460-chr6:31731403..31733722,2	MCF-7	breast:
8	chr6:31647892..31650324-chr6:31793249..31795639,4	MCF-7	breast:
9	chr6:31647222..31652409-chr6:31701244..31706736,11	MCF-7	breast:
10	chr6:31646374..31649912-chr6:31794618..31797680,6	MCF-7	breast:
11	chr6:31617977..31621822-chr6:31647367..31651078,5	MCF-7	breast:
12	chr6:31646441..31651407-chr6:31704606..31708985,8	MCF-7	breast:
13	chr6:31648224..31648787-chr6:31758999..31759731,2	MCF-7	breast:
14	chr6:31647152..31650140-chr6:31654951..31659176,4	MCF-7	breast:
15	chr6:31647696..31650047-chr6:31656817..31658939,2	MCF-7	breast:
16	chr6:31646338..31652560-chr6:31697885..31704222,10	MCF-7	breast:
17	chr6:31513206..31515445-chr6:31647940..31649568,2	MCF-7	breast:
18	chr6:31647774..31650438-chr6:31800193..31802973,5	MCF-7	breast:
19	chr6:31648169..31649094-chr6:31740479..31741224,2	K562	blood:

No data

Variant related genes	Relation type
LY6G5C	TF binding region
ENSG00000254870	Chromatin interaction
ENSG00000204410	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000255152	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000113594	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000235663	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204394	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1046089	0.82[ASN][1000 genomes]
rs1052486	0.87[ASN][1000 genomes]
rs1077393	0.87[ASN][1000 genomes]
rs1266075	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1266076	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2077491	0.85[ASN][1000 genomes]
rs2242659	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2242660	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2260000	0.80[ASN][1000 genomes]
rs2736155	0.85[ASN][1000 genomes]
rs2844465	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2844466	0.82[ASN][1000 genomes]
rs4569	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7029	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7992	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805257	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs805262	0.82[ASN][1000 genomes]
rs805271	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805277	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805282	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805287	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805288	0.83[EUR][1000 genomes]
rs805301	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs805302	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs805303	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs813115	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs805290	CSNK2B	cis	lymphoblastoid	seeQTL
rs805290	GRM4	cis	cerebellum	SCAN
rs805290	AIF1	Cis_1M	lymphoblastoid	RTeQTL
rs805290	LY6G5C	cis	Cerebellum	GTEx
rs805290	BAT4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31640200-31648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:31640200-31648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:31641400-31648800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:31641400-31648800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:31641400-31648800	Weak transcription	Aorta	Aorta
6	chr6:31641400-31648800	Weak transcription	Ovary	ovary
7	chr6:31641400-31654000	Weak transcription	Dnd41	blood
8	chr6:31641600-31648600	Weak transcription	Fetal Brain Female	brain
9	chr6:31642000-31649000	Weak transcription	Gastric	stomach
10	chr6:31644600-31648600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:31647200-31648600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:31647800-31648800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:31647800-31648800	Enhancers	NHLF	lung
14	chr6:31648000-31648600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:31648000-31648600	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:31648000-31648600	Enhancers	Colonic Mucosa	Colon
17	chr6:31648000-31648600	Enhancers	Colon Smooth Muscle	Colon
18	chr6:31648000-31648600	Enhancers	Fetal Muscle Leg	muscle
19	chr6:31648000-31648800	Enhancers	Fetal Stomach	stomach
20	chr6:31648000-31648800	Enhancers	HSMMtube	muscle
21	chr6:31648000-31649000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:31648000-31649600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr6:31648000-31649800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr6:31648000-31649800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:31648200-31648600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:31648200-31648600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:31648200-31648600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr6:31648200-31648600	Enhancers	Primary B cells from cord blood	blood
29	chr6:31648200-31648600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr6:31648200-31648600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:31648200-31648600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:31648200-31648600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:31648200-31648600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:31648200-31648600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:31648200-31648600	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr6:31648200-31648600	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr6:31648200-31648600	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr6:31648200-31648600	Enhancers	Fetal Intestine Small	intestine
39	chr6:31648200-31648600	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr6:31648200-31648600	Enhancers	Right Ventricle	heart
41	chr6:31648200-31648600	Enhancers	Spleen	Spleen
42	chr6:31648200-31648600	Flanking Active TSS	Hela-S3	cervix
43	chr6:31648200-31648600	Enhancers	HMEC	breast
44	chr6:31648200-31648600	Flanking Active TSS	NHDF-Ad	bronchial
45	chr6:31648200-31648800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:31648200-31648800	Enhancers	Esophagus	oesophagus
47	chr6:31648200-31648800	Enhancers	Fetal Intestine Large	intestine
48	chr6:31648200-31648800	Enhancers	Placenta	Placenta
49	chr6:31648200-31648800	Enhancers	HSMM	muscle
50	chr6:31648200-31649400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links