Variant report

Variant	rs3016316
Chromosome Location	chr11:66104057-66104058
allele	A/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	FOS	chr11:66103734-66104533	HUVEC	blood vessel:	n/a	chr11:66104295-66104302 chr11:66104294-66104303 chr11:66104295-66104303 chr11:66104293-66104305 chr11:66104293-66104304 chr11:66104294-66104304
2	POLR2A	chr11:66102843-66104643	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:66104023-66104516	K562	blood:	n/a	n/a
4	NFATC1	chr11:66103886-66104494	GM12878	blood:	n/a	chr11:66104355-66104368
5	PBX3	chr11:66103190-66104643	A549	lung:	n/a	n/a
6	POLR2A	chr11:66103558-66104599	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr11:66103123-66104597	HepG2	liver:	n/a	n/a
8	CTCF	chr11:66104008-66104569	K562	blood:	n/a	chr11:66104268-66104289 chr11:66104274-66104290 chr11:66104421-66104431 chr11:66104273-66104291
9	CHD2	chr11:66103672-66104412	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:66102818-66104682	MCF-7	breast:	n/a	n/a
11	HCFC1	chr11:66102619-66104575	Hela-S3	cervix:	n/a	n/a
12	RFX5	chr11:66104005-66104515	HepG2	liver:	n/a	chr11:66104354-66104369 chr11:66104354-66104369 chr11:66104328-66104342 chr11:66104327-66104342 chr11:66104354-66104369 chr11:66104331-66104340 chr11:66104330-66104345
13	GABPA	chr11:66103965-66104397	K562	blood:	n/a	n/a
14	E2F4	chr11:66103900-66104509	MCF10A-Er-Src	breast:	n/a	chr11:66104154-66104166
15	MAX	chr11:66102800-66104675	HepG2	liver:	n/a	chr11:66104147-66104162 chr11:66104331-66104340 chr11:66104151-66104160 chr11:66104359-66104368 chr11:66104355-66104364 chr11:66104294-66104303 chr11:66104295-66104304
16	CTCF	chr11:66104009-66104437	K562	blood:	n/a	chr11:66104268-66104289 chr11:66104274-66104290 chr11:66104421-66104431 chr11:66104273-66104291
17	EBF1	chr11:66103897-66104672	GM12878	blood:	n/a	chr11:66104202-66104213
18	MAX	chr11:66103754-66104604	K562	blood:	n/a	chr11:66104147-66104162 chr11:66104331-66104340 chr11:66104151-66104160 chr11:66104359-66104368 chr11:66104355-66104364 chr11:66104294-66104303 chr11:66104295-66104304
19	NR2F2	chr11:66103842-66104572	K562	blood:	n/a	n/a
20	POLR2A	chr11:66103017-66104311	HUVEC	blood vessel:	n/a	n/a
21	MXI1	chr11:66102626-66105682	SK-N-SH	brain:	n/a	chr11:66104331-66104346 chr11:66104355-66104370 chr11:66104353-66104368
22	POLR2A	chr11:66103764-66104561	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:66103823-66104626	GM12891	blood:	n/a	n/a
24	MYC	chr11:66103717-66104519	HUVEC	blood vessel:	n/a	chr11:66104147-66104162 chr11:66104331-66104340 chr11:66104151-66104160 chr11:66104359-66104368 chr11:66104355-66104364 chr11:66104294-66104303 chr11:66104295-66104304
25	FOS	chr11:66103789-66104655	MCF10A-Er-Src	breast:	n/a	chr11:66104295-66104302 chr11:66104294-66104303 chr11:66104295-66104303 chr11:66104293-66104305 chr11:66104293-66104304 chr11:66104294-66104304
26	USF1	chr11:66103794-66104400	SK-N-SH	brain:	n/a	n/a
27	MAFF	chr11:66103994-66104524	HepG2	liver:	n/a	n/a
28	POLR2A	chr11:66103427-66104685	PANC-1	pancreas:	n/a	n/a
29	CHD2	chr11:66103217-66104430	Hela-S3	cervix:	n/a	n/a
30	ZBTB7A	chr11:66103910-66104363	K562	blood:	n/a	n/a
31	ARID3A	chr11:66103997-66104381	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:66101875-66105316	IMR90	lung:	n/a	n/a
33	POLR2A	chr11:66103660-66104817	GM12878	blood:	n/a	n/a
34	TCF3	chr11:66104009-66104166	GM12878	blood:	n/a	n/a
35	CBX3	chr11:66104001-66104446	K562	blood:	n/a	n/a
36	MAX	chr11:66102996-66104706	HepG2	liver:	n/a	chr11:66104147-66104162 chr11:66104331-66104340 chr11:66104151-66104160 chr11:66104359-66104368 chr11:66104355-66104364 chr11:66104294-66104303 chr11:66104295-66104304
37	BCLAF1	chr11:66103855-66104498	GM12878	blood:	n/a	chr11:66104295-66104304 chr11:66104294-66104303
38	FOXA1	chr11:66103894-66104520	HepG2	liver:	n/a	n/a
39	POLR2A	chr11:66102730-66104638	U87	brain:	n/a	n/a
40	ZBTB7A	chr11:66104040-66104333	HepG2	liver:	n/a	n/a
41	EBF1	chr11:66103939-66104631	GM12878	blood:	n/a	chr11:66104202-66104213
42	EGR1	chr11:66103991-66104272	GM12878	blood:	n/a	chr11:66104151-66104161 chr11:66104151-66104161 chr11:66104152-66104161 chr11:66104149-66104163 chr11:66104207-66104231
43	EGR1	chr11:66103824-66104689	MCF-7	breast:	n/a	chr11:66104468-66104490 chr11:66104474-66104484 chr11:66104479-66104488 chr11:66104474-66104485 chr11:66104151-66104161 chr11:66104474-66104484 chr11:66104151-66104161 chr11:66104473-66104486 chr11:66103945-66103954 chr11:66104152-66104161 chr11:66104149-66104163 chr11:66104207-66104231 chr11:66104472-66104486 chr11:66104474-66104485
44	ELF1	chr11:66103378-66104355	GM12878	blood:	n/a	n/a
45	GABPA	chr11:66103500-66104400	MCF-7	breast:	n/a	n/a
46	POU2F2	chr11:66103783-66104629	GM12878	blood:	n/a	n/a
47	MXI1	chr11:66104005-66104599	GM12878	blood:	n/a	chr11:66104331-66104346 chr11:66104355-66104370 chr11:66104353-66104368
48	RAD21	chr11:66103793-66104503	HepG2	liver:	n/a	chr11:66104271-66104290 chr11:66104451-66104463
49	ZEB1	chr11:66103950-66104319	GM12878	blood:	n/a	n/a
50	MXI1	chr11:66103468-66104559	HepG2	liver:	n/a	chr11:66104331-66104346 chr11:66104355-66104370 chr11:66104353-66104368

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:66104018-66104068	BE2_C	brain:	n/a
2	chr11:66104018-66104068	AG10803	skin:	n/a
3	chr11:66104018-66104068	HepG2	liver:	n/a
4	chr11:66104018-66104068	NHDF-neo	bronchial:	n/a
5	chr11:66104018-66104068	CMK	blood:	n/a
6	chr11:66104018-66104068	MCF10A-Er-Src	breast:	n/a
7	chr11:66104018-66104068	HPAEpiC	pulmonary alveolar:	n/a
8	chr11:66104018-66104068	HRPEpiC	eye:	n/a
9	chr11:66104018-66104068	LNCaP	prostate:	n/a
10	chr11:66104018-66104068	Hela-S3	cervix:	n/a
11	chr11:66104018-66104068	BJ	skin:	n/a
12	chr11:66104018-66104068	SAEC	small airway:	n/a
13	chr11:66104018-66104068	HRCEpiC	kidney:	n/a
14	chr11:66104018-66104068	AG09309	skin:	n/a
15	chr11:66104018-66104068	GM12891	blood:	n/a
16	chr11:66104018-66104068	HCPEpiC	choroid plexus:	n/a
17	chr11:66104018-66104068	HL-60	blood:	n/a
18	chr11:66104018-66104068	HCM	heart:	n/a
19	chr11:66104018-66104068	NT2-D1	testis:	n/a
20	chr11:66104018-66104068	IMR90	lung:	fetal
21	chr11:66104018-66104068	HAEpiC	amniotic membrane:	n/a
22	chr11:66104018-66104068	SKMC	muscle:	n/a
23	chr11:66104018-66104068	SK-N-SH_RA	brain:	n/a
24	chr11:66104018-66104068	Caco-2	colon:	n/a
25	chr11:66104018-66104068	HRE	kidney:	n/a
26	chr11:66104018-66104068	Hepatocyte	liver:	n/a
27	chr11:66104018-66104068	GM12878	blood:	n/a
28	chr11:66104018-66104068	HEEpiC	esophagus:	n/a
29	chr11:66104018-66104068	AG04449	skin:	fetal
30	chr11:66104018-66104068	PFSK-1	brain:	n/a
31	chr11:66104018-66104068	H1-hESC	embryonic stem cell:	embryo
32	chr11:66104018-66104068	Jurkat	blood:	n/a
33	chr11:66104018-66104068	HCT-116	colon:	n/a
34	chr11:66104018-66104068	HIPEpiC	eye:	n/a
35	chr11:66104018-66104068	ECC-1	luminal epithelium:	n/a
36	chr11:66104018-66104068	GM12892	blood:	n/a
37	chr11:66104018-66104068	AG09319	gingival:	n/a
38	chr11:66104018-66104068	RPTEC	kidney:	n/a
39	chr11:66104018-66104068	GM06990	blood:	n/a
40	chr11:66104018-66104068	NHBE	bronchial:	n/a
41	chr11:66104018-66104068	A549	lung:	n/a
42	chr11:66104018-66104068	SK-N-MC	brain:	n/a
43	chr11:66104018-66104068	GM19239	blood:	n/a
44	chr11:66104018-66104068	ovcar-3	ovarian:	n/a
45	chr11:66104018-66104068	PANC-1	pancreas:	n/a
46	chr11:66104018-66104068	HNPCEpiC	eye:	n/a
47	chr11:66104018-66104068	K562	blood:	n/a
48	chr11:66104018-66104068	NB4	blood:	n/a
49	chr11:66104018-66104068	SK-N-SH	brain:	n/a
50	chr11:66104018-66104068	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66055819..66057691-chr11:66103911..66105498,2	K562	blood:
2	chr11:66052249..66054204-chr11:66103456..66106375,2	K562	blood:
3	chr11:66077376..66081785-chr11:66101114..66107038,7	MCF-7	breast:
4	chr11:66053447..66056540-chr11:66100445..66105768,7	MCF-7	breast:
5	chr11:66102581..66106910-chr11:66137391..66141246,5	MCF-7	breast:
6	chr11:66083086..66084913-chr11:66102353..66104167,3	MCF-7	breast:
7	chr11:66102037..66105089-chr11:66137738..66140850,8	MCF-7	breast:
8	chr11:66103854..66118324-chr11:66119048..66141728,55	K562	blood:
9	chr11:66055597..66057691-chr11:66102656..66105498,2	K562	blood:
10	chr11:66103394..66104172-chr11:118888520..118889037,2	NB4	blood:

Variant related genes	Relation type
RIN1	TF binding region
RIN1	CpG island
ENSG00000174807	Chromatin interaction
ENSG00000174669	Chromatin interaction
ENSG00000174851	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000118181	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11537930	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1190621	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1190622	0.93[EUR][1000 genomes]
rs1190623	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1212135	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016960	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2186596	0.80[ASN][1000 genomes]
rs3016311	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3016317	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814740	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4390351	0.82[ASN][1000 genomes]
rs56240803	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57004348	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58221849	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59651473	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950463	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948360	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv897781	chr11:66095967-66116911	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv1813137	chr11:66098322-66106725	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
9	nsv897782	chr11:66099222-66116911	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	esv1850142	chr11:66099494-66105817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3016316	RP11-867G23.12	cis	Whole Blood	GTEx
rs3016316	RIN1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66096400-66104400	Weak transcription	Dnd41	blood
2	chr11:66098400-66108800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:66102200-66105000	Flanking Active TSS	NH-A	brain
4	chr11:66102400-66104400	Enhancers	Primary B cells from cord blood	blood
5	chr11:66102400-66104400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr11:66102400-66104600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr11:66102600-66104200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:66102600-66104200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:66102600-66104200	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr11:66102600-66104200	Enhancers	GM12878-XiMat	blood
11	chr11:66102600-66104600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr11:66102800-66104200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr11:66102800-66104200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr11:66102800-66104200	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr11:66102800-66104200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr11:66102800-66104200	Flanking Active TSS	Pancreas	Pancrea
17	chr11:66102800-66104200	Flanking Active TSS	Right Ventricle	heart
18	chr11:66102800-66104200	Flanking Active TSS	HUVEC	blood vessel
19	chr11:66102800-66104400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:66102800-66104400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:66102800-66104400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr11:66102800-66104400	Flanking Active TSS	Colonic Mucosa	Colon
23	chr11:66102800-66104400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr11:66102800-66104400	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr11:66102800-66104400	Enhancers	K562	blood
26	chr11:66102800-66104600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr11:66102800-66105000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:66103000-66104200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:66103000-66104200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr11:66103000-66104200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr11:66103000-66104200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:66103000-66104200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:66103000-66104200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr11:66103000-66104200	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr11:66103000-66104400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr11:66103000-66104400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:66103000-66104400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr11:66103000-66104400	Flanking Active TSS	Esophagus	oesophagus
39	chr11:66103000-66104400	Flanking Active TSS	Fetal Lung	lung
40	chr11:66103000-66104400	Flanking Active TSS	Placenta	Placenta
41	chr11:66103200-66104200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:66103200-66104600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:66103200-66104600	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr11:66103400-66104200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr11:66103400-66104400	Active TSS	Fetal Kidney	kidney
46	chr11:66103400-66104600	Enhancers	Fetal Heart	heart
47	chr11:66103400-66104800	Flanking Active TSS	Osteobl	bone
48	chr11:66103400-66106200	Enhancers	Fetal Brain Male	brain
49	chr11:66103600-66104200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:66103600-66104200	Flanking Active TSS	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links