Variant report

Variant	rs35480350
Chromosome Location	chr16:30366039-30366040
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	SIN3AK20	chr16:30365977-30367347	HepG2	liver:	n/a	n/a
2	PML	chr16:30365941-30367409	K562	blood:	n/a	n/a
3	MAX	chr16:30366004-30368463	A549	lung:	n/a	chr16:30366283-30366292 chr16:30368180-30368187 chr16:30367527-30367536 chr16:30366756-30366765 chr16:30366283-30366292 chr16:30366283-30366292 chr16:30368179-30368188 chr16:30366282-30366293 chr16:30367525-30367540
4	STAT5A	chr16:30365704-30367771	GM12878	blood:	n/a	chr16:30367034-30367042 chr16:30366422-30366430 chr16:30366058-30366070
5	POLR2A	chr16:30365903-30368374	GM12892	blood:	n/a	n/a
6	HCFC1	chr16:30365561-30368232	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr16:30365855-30367651	H1-neurons	neurons:	n/a	n/a
8	GABPA	chr16:30365588-30367804	MCF-7	breast:	n/a	n/a
9	POLR2A	chr16:30365895-30367998	H1-neurons	neurons:	n/a	n/a
10	MAX	chr16:30365898-30367747	K562	blood:	n/a	chr16:30366283-30366292 chr16:30367527-30367536 chr16:30366756-30366765 chr16:30366283-30366292 chr16:30366283-30366292 chr16:30366282-30366293 chr16:30367525-30367540
11	RUNX3	chr16:30365961-30367706	GM12878	blood:	n/a	n/a
12	CHD1	chr16:30366015-30366215	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr16:30365702-30367655	H1-neurons	neurons:	n/a	chr16:30367280-30367300 chr16:30366224-30366237 chr16:30366371-30366384
14	SIN3A	chr16:30365820-30367385	H1-hESC	embryonic stem cell:	n/a	chr16:30366371-30366384 chr16:30366284-30366293 chr16:30366755-30366764
15	PML	chr16:30365948-30368023	GM12878	blood:	n/a	n/a
16	MAX	chr16:30365799-30367795	HCT-116	colon:	n/a	chr16:30366283-30366292 chr16:30367527-30367536 chr16:30366756-30366765 chr16:30366283-30366292 chr16:30366283-30366292 chr16:30366282-30366293 chr16:30367525-30367540
17	ELF1	chr16:30365870-30367761	HCT-116	colon:	n/a	chr16:30366646-30366655 chr16:30366823-30366836 chr16:30366645-30366656 chr16:30366377-30366389 chr16:30366645-30366656
18	BACH1	chr16:30366016-30366145	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF7	chr16:30366030-30367357	H1-hESC	embryonic stem cell:	n/a	n/a
20	TCF12	chr16:30365680-30367814	A549	lung:	n/a	chr16:30367370-30367379
21	POLR2A	chr16:30365719-30368371	K562	blood:	n/a	n/a
22	MYBL2	chr16:30365570-30367820	HepG2	liver:	n/a	n/a
23	POLR2A	chr16:30365973-30367577	Hela-S3	cervix:	n/a	n/a
24	SIN3AK20	chr16:30365840-30367351	SK-N-SH	brain:	n/a	n/a
25	GABPA	chr16:30366019-30367467	A549	lung:	n/a	n/a
26	ELK1	chr16:30366025-30366160	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr16:30365759-30367303	IMR90	lung:	n/a	n/a
28	POLR2A	chr16:30365748-30368408	K562	blood:	n/a	n/a
29	POLR2A	chr16:30365726-30368332	U87	brain:	n/a	n/a
30	POLR2A	chr16:30365846-30367907	HUVEC	blood vessel:	n/a	n/a
31	GABPA	chr16:30365950-30367415	MCF-7	breast:	n/a	n/a
32	POLR2A	chr16:30360110-30369693	HepG2	liver:	n/a	n/a
33	MAX	chr16:30365806-30367847	HepG2	liver:	n/a	chr16:30366283-30366292 chr16:30367527-30367536 chr16:30366756-30366765 chr16:30366283-30366292 chr16:30366283-30366292 chr16:30366282-30366293 chr16:30367525-30367540
34	TEAD4	chr16:30365746-30366165	K562	blood:	n/a	n/a
35	YY1	chr16:30366030-30367615	HepG2	liver:	n/a	chr16:30366307-30366321
36	USF1	chr16:30365980-30367080	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr16:30366000-30367404	HepG2	liver:	n/a	n/a
38	FOSL2	chr16:30365138-30367884	HepG2	liver:	n/a	chr16:30366747-30366756 chr16:30365766-30365777 chr16:30365838-30365847
39	POLR2A	chr16:30366023-30367631	GM12892	blood:	n/a	n/a
40	ELF1	chr16:30365592-30366040	K562	blood:	n/a	chr16:30365699-30365710
41	ZKSCAN1	chr16:30365979-30366076	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr16:30365516-30367499	IMR90	lung:	n/a	chr16:30366283-30366292 chr16:30366756-30366765 chr16:30366283-30366292 chr16:30366283-30366292 chr16:30366282-30366293
43	POLR2A	chr16:30365939-30368340	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr16:30365726-30368558	K562	blood:	n/a	n/a
45	SMC3	chr16:30365927-30366217	HepG2	liver:	n/a	n/a
46	RCOR1	chr16:30366026-30367337	HepG2	liver:	n/a	n/a
47	POLR2A	chr16:30366032-30367928	H1-hESC	embryonic stem cell:	n/a	n/a
48	NFIC	chr16:30365786-30366269	HepG2	liver:	n/a	n/a
49	POLR2A	chr16:30361391-30369063	HepG2	liver:	n/a	n/a
50	POLR2A	chr16:30365980-30367884	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30365313..30367848-chr16:30618924..30623102,3	MCF-7	breast:
2	chr16:30364578..30368660-chr16:30404559..30407754,8	MCF-7	breast:
3	chr16:30365100..30369727-chr16:30387622..30391726,6	MCF-7	breast:
4	chr16:30345336..30346987-chr16:30364992..30366777,2	K562	blood:
5	chr16:30345346..30347194-chr16:30364689..30366452,2	MCF-7	breast:
6	chr16:30365182..30368523-chr16:30417932..30420526,3	K562	blood:
7	chr16:30364489..30367608-chr16:30429426..30432189,3	K562	blood:
8	chr16:30365632..30367992-chr16:30667854..30670358,2	MCF-7	breast:
9	chr16:30107356..30109968-chr16:30365959..30368082,2	MCF-7	breast:
10	chr16:30106190..30107889-chr16:30365299..30366898,2	K562	blood:
11	chr16:30364739..30368463-chr16:30416926..30421783,8	MCF-7	breast:
12	chr16:30364152..30368341-chr16:30388051..30392327,13	K562	blood:
13	chr16:30364744..30367445-chr17:58469119..58471107,2	MCF-7	breast:
14	chr16:30366000..30368960-chr16:68270888..68273271,2	MCF-7	breast:
15	chr16:30076995..30078721-chr16:30365151..30368366,3	MCF-7	breast:
16	chr16:30364024..30368341-chr16:30387690..30394486,12	K562	blood:
17	chr16:30365775..30369229-chr16:30392373..30394486,5	K562	blood:

Variant related genes	Relation type
ENSG00000260219	TF binding region
ENSG00000103067	Chromatin interaction
ENSG00000250616	Chromatin interaction
ENSG00000156853	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000199787	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000179965	Chromatin interaction
ENSG00000183604	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000261469	Chromatin interaction
ENSG00000090238	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000170832	Chromatin interaction
ENSG00000270466	Chromatin interaction
ENSG00000141371	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11150586	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1132812	1.00[YRI][hapmap]
rs11642676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644392	0.90[ASN][1000 genomes]
rs11645581	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11646130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11863150	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs12446288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs12447833	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12921440	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12922786	0.88[ASN][1000 genomes]
rs12930787	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13331817	0.88[GIH][hapmap];0.85[YRI][hapmap]
rs13333093	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2911213	0.87[ASN][1000 genomes]
rs35598865	1.00[JPT][hapmap]
rs3574	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4465620	0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs4471699	0.93[ASN][1000 genomes]
rs4787642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4787643	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4788408	0.93[ASN][1000 genomes]
rs4788409	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4788413	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62055459	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6565176	0.88[GIH][hapmap]
rs6565178	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6565180	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68051857	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7186541	0.90[ASN][1000 genomes]
rs7195216	0.90[ASN][1000 genomes]
rs7203359	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73532600	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7404371	0.88[ASN][1000 genomes]
rs8046445	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8049108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8050176	0.93[ASN][1000 genomes]
rs8050812	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs8051096	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8060853	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9921711	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs35480350	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs35480350	SEPHS2	cis	cerebellum	SCAN
rs35480350	GDPD3	cis	cerebellum	SCAN
rs35480350	MAPK3	cis	parietal	SCAN
rs35480350	TBX6	cis	parietal	SCAN
rs35480350	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30364400-30371800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:30364800-30366200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr16:30365200-30366200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr16:30365200-30366200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:30365200-30366200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr16:30365200-30366200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
7	chr16:30365400-30366200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr16:30365400-30366200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr16:30365400-30366200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr16:30365400-30366200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr16:30365400-30366200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr16:30365400-30366200	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr16:30365400-30366200	Flanking Active TSS	Brain Substantia Nigra	brain
14	chr16:30365400-30366200	Flanking Active TSS	Colonic Mucosa	Colon
15	chr16:30365400-30366200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr16:30365400-30366200	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr16:30365400-30366200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr16:30365400-30366400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
19	chr16:30365400-30366400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr16:30365400-30366400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr16:30365400-30366400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr16:30365400-30366400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr16:30365400-30367400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr16:30365400-30367600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:30365400-30367800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr16:30365400-30367800	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr16:30365400-30368000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:30365600-30366200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr16:30365600-30366200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr16:30365600-30366200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr16:30365600-30366200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr16:30365600-30366200	Flanking Active TSS	Liver	Liver
33	chr16:30365600-30366200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr16:30365600-30366200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr16:30365600-30366200	Flanking Active TSS	Fetal Brain Female	brain
36	chr16:30365600-30366200	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr16:30365600-30366200	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr16:30365600-30366200	Flanking Active TSS	Fetal Thymus	thymus
39	chr16:30365600-30366200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr16:30365600-30366200	Transcr. at gene 5' and 3'	Thymus	Thymus
41	chr16:30365600-30366400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr16:30365600-30366600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr16:30365600-30366800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr16:30365600-30367000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr16:30365600-30367000	Active TSS	NHDF-Ad	bronchial
46	chr16:30365600-30367200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr16:30365600-30367200	Active TSS	Esophagus	oesophagus
48	chr16:30365600-30367200	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr16:30365600-30367400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr16:30365600-30367400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links