Variant report

Variant	rs16835846
Chromosome Location	chr1:154127736-154127737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154126848-154127883	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:154127428-154128204	K562	blood:	n/a	n/a
3	POLR2A	chr1:154126201-154128392	U87	brain:	n/a	n/a
4	POLR2A	chr1:154126673-154128315	HUVEC	blood vessel:	n/a	n/a
5	CHD2	chr1:154127457-154127755	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:154126850-154128357	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:154126077-154128299	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:154126931-154128239	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:154126957-154128168	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:154127726-154127742	MCF-7	breast:	n/a	n/a
11	POLR2A	chr1:154126854-154128608	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr1:154127370-154128385	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:154126751-154128167	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:154126532-154128374	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:154127736-154127746	K562	blood:	n/a	n/a
16	POLR2A	chr1:154127441-154127745	HCT-116	colon:	n/a	n/a
17	POLR2A	chr1:154126934-154127770	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:154127360-154128463	GM12892	blood:	n/a	n/a
19	GATA1	chr1:154127472-154128477	PBDE	blood:	n/a	n/a
20	POLR2A	chr1:154126745-154128076	GM12891	blood:	n/a	n/a
21	CREB1	chr1:154127273-154127854	H1-hESC	embryonic stem cell:	n/a	chr1:154127589-154127602
22	POLR2A	chr1:154126091-154128677	PFSK-1	brain:	n/a	n/a
23	PML	chr1:154126861-154128129	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:154126291-154127743	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr1:154127344-154128436	K562	blood:	n/a	n/a
26	CCNT2	chr1:154127508-154128008	K562	blood:	n/a	n/a
27	RFX5	chr1:154127391-154127755	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:154127729-154128193	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr1:154126919-154128203	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:154126883-154128299	HL-60	blood:	n/a	n/a
31	POLR2A	chr1:154126172-154128709	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr1:154126858-154128169	HL-60	blood:	n/a	n/a
33	CREB1	chr1:154127332-154127837	H1-hESC	embryonic stem cell:	n/a	chr1:154127589-154127602
34	POLR2A	chr1:154126447-154128372	A549	lung:	n/a	n/a
35	POLR2A	chr1:154126938-154128434	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:154127212-154128352	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr1:154126411-154128102	GM12891	blood:	n/a	n/a
38	CHD1	chr1:154127422-154127791	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr1:154126864-154128753	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:154126284-154128518	K562	blood:	n/a	n/a
41	ATF2	chr1:154127339-154127770	H1-hESC	embryonic stem cell:	n/a	chr1:154127590-154127601
42	POLR2A	chr1:154126845-154129319	GM12892	blood:	n/a	n/a
43	MTA3	chr1:154126661-154128099	GM12878	blood:	n/a	n/a
44	MYC	chr1:154127710-154127771	K562	blood:	n/a	n/a
45	POLR2A	chr1:154126260-154127848	U87	brain:	n/a	n/a
46	ZMIZ1	chr1:154127638-154127836	K562	blood:	n/a	n/a
47	E2F6	chr1:154126932-154127866	H1-hESC	embryonic stem cell:	n/a	chr1:154127590-154127599 chr1:154127592-154127601
48	POLR2A	chr1:154126950-154128184	Hela-S3	cervix:	n/a	n/a
49	TBL1XR1	chr1:154127525-154127828	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154122896..154125457-chr1:154127729..154131254,3	MCF-7	breast:

No data

Variant related genes	Relation type
NUP210L	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158820	0.87[JPT][hapmap]
rs1044013	0.87[JPT][hapmap]
rs1113142	0.84[YRI][hapmap]
rs11265238	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11265251	0.87[JPT][hapmap]
rs11265425	0.91[JPT][hapmap]
rs11802893	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1194593	0.86[JPT][hapmap]
rs1194594	0.92[YRI][hapmap]
rs1194596	0.87[JPT][hapmap]
rs1194597	0.82[YRI][hapmap]
rs1194601	0.91[YRI][hapmap]
rs1194605	0.87[YRI][hapmap]
rs12025237	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs12026177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026615	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs12028949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038362	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs1205590	0.87[YRI][hapmap]
rs12062977	0.87[JPT][hapmap]
rs16835852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1685625	0.80[YRI][hapmap]
rs1760802	0.87[JPT][hapmap]
rs2274993	0.81[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs2340473	0.82[JPT][hapmap]
rs2500222	0.91[YRI][hapmap]
rs2633434	0.95[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap]
rs28372838	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2879788	0.87[JPT][hapmap]
rs3002660	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34128679	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34335016	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35761479	0.84[EUR][1000 genomes]
rs3762340	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs3790613	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs3811453	0.90[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs3811455	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3828077	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs3935419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433384	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs4620534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60282844	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427509	0.86[JPT][hapmap]
rs6666943	0.84[YRI][hapmap]
rs6673752	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs6676022	0.82[EUR][1000 genomes]
rs6719	0.87[JPT][hapmap]
rs715737	0.84[YRI][hapmap]
rs9803857	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16835846	DENND4B	cis	parietal	SCAN
rs16835846	SLC27A3	cis	lymphoblastoid	seeQTL
rs16835846	RAB13	cis	parietal	SCAN
rs16835846	HAX1	cis	parietal	SCAN
rs16835846	HAX1	cis	lymphoblastoid	seeQTL
rs16835846	HAX1	cis	cerebellum	SCAN
rs16835846	PIP5K1A	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154124000-154127800	Weak transcription	Small Intestine	intestine
3	chr1:154124000-154128000	Weak transcription	NHDF-Ad	bronchial
4	chr1:154124400-154129800	Weak transcription	Left Ventricle	heart
5	chr1:154125000-154130400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:154125200-154131000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:154125400-154128000	Weak transcription	Stomach Mucosa	stomach
8	chr1:154125600-154128000	Weak transcription	NHEK	skin
9	chr1:154125600-154129800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:154125600-154129800	Weak transcription	Gastric	stomach
11	chr1:154125600-154130000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:154125800-154129600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:154126000-154128000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:154126200-154128200	Genic enhancers	Primary T cells from cord blood	blood
15	chr1:154126200-154128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:154126200-154128800	Genic enhancers	Primary hematopoietic stem cells	blood
17	chr1:154126200-154128800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:154126200-154129400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:154126200-154129400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:154126200-154129600	Weak transcription	HSMMtube	muscle
21	chr1:154126200-154130400	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr1:154126400-154127800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:154126400-154128600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:154126400-154128600	Strong transcription	Thymus	Thymus
25	chr1:154126400-154129600	Genic enhancers	K562	blood
26	chr1:154126400-154129600	Genic enhancers	NHLF	lung
27	chr1:154126400-154129800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:154126400-154129800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:154126400-154130400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:154126400-154133000	Weak transcription	Ovary	ovary
31	chr1:154126400-154146000	Strong transcription	HMEC	breast
32	chr1:154126600-154128200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:154126600-154129600	Weak transcription	HepG2	liver
34	chr1:154126600-154130200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:154126800-154127800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:154126800-154127800	Weak transcription	NH-A	brain
37	chr1:154126800-154128600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:154126800-154129800	Strong transcription	GM12878-XiMat	blood
39	chr1:154126800-154130000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:154126800-154130200	Weak transcription	Fetal Brain Male	brain
41	chr1:154126800-154131600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:154127000-154127800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:154127000-154127800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:154127000-154127800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:154127000-154127800	Enhancers	Pancreas	Pancrea
46	chr1:154127000-154127800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:154127000-154127800	Strong transcription	A549	lung
48	chr1:154127000-154128000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:154127000-154128200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:154127000-154128200	Genic enhancers	Fetal Stomach	stomach

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