Variant report

Variant	rs7161368
Chromosome Location	chr14:67983868-67983869
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	CTCF	chr14:67983840-67983990	HA-sp	spinal cord:	n/a	n/a
2	RAD21	chr14:67983866-67984111	HepG2	liver:	n/a	chr14:67983924-67983936
3	RAD21	chr14:67983747-67984196	MCF-7	breast:	n/a	chr14:67983924-67983936
4	RAD21	chr14:67983732-67984196	H1-hESC	embryonic stem cell:	n/a	chr14:67983924-67983936
5	RAD21	chr14:67983808-67984117	HepG2	liver:	n/a	chr14:67983924-67983936
6	CTCF	chr14:67983740-67983890	HPF	lung:	n/a	n/a
7	RAD21	chr14:67983718-67984215	HCT-116	colon:	n/a	chr14:67983924-67983936
8	RAD21	chr14:67983807-67984221	A549	lung:	n/a	chr14:67983924-67983936
9	RAD21	chr14:67983751-67984196	HCT-116	colon:	n/a	chr14:67983924-67983936
10	SMC3	chr14:67983824-67984024	HepG2	liver:	n/a	n/a
11	CTCF	chr14:67983840-67983990	BE2_C	brain:	n/a	n/a
12	RAD21	chr14:67983771-67984206	ECC-1	luminal epithelium:	n/a	chr14:67983924-67983936
13	RAD21	chr14:67983785-67984220	HepG2	liver:	n/a	chr14:67983924-67983936
14	CTCF	chr14:67983866-67984148	A549	lung:	n/a	n/a
15	CTCF	chr14:67983836-67984218	K562	blood:	n/a	n/a
16	CTCF	chr14:67983860-67984010	BE2_C	brain:	n/a	n/a
17	CTCF	chr14:67983840-67983990	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr14:67983835-67984108	T-47D	breast:	n/a	n/a
19	MAX	chr14:67983409-67983996	NB4	blood:	n/a	chr14:67983591-67983602 chr14:67983593-67983600 chr14:67983591-67983601 chr14:67983591-67983602 chr14:67983592-67983602 chr14:67983592-67983601 chr14:67983592-67983601 chr14:67983592-67983602 chr14:67983591-67983602
20	RAD21	chr14:67983831-67984196	H1-hESC	embryonic stem cell:	n/a	chr14:67983924-67983936
21	CTCF	chr14:67983806-67984148	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr14:67983788-67984176	SK-N-SH_RA	brain:	n/a	chr14:67983924-67983936
23	RAD21	chr14:67983843-67984167	H1-hESC	embryonic stem cell:	n/a	chr14:67983924-67983936
24	CTCF	chr14:67983864-67984090	HepG2	liver:	n/a	n/a
25	RAD21	chr14:67983862-67984187	IMR90	lung:	n/a	chr14:67983924-67983936

No.	Distal block	Cell Line	Cell type
1	chr14:67982264..67984804-chr14:68036407..68038355,2	MCF-7	breast:
2	chr14:67980933..67983898-chr14:67998089..68001326,3	MCF-7	breast:
3	chr14:67983855..67986237-chr14:67998798..68001170,2	K562	blood:
4	chr14:67953824..67955734-chr14:67983233..67985363,2	MCF-7	breast:

Variant related genes	Relation type
TMEM229B	TF binding region
ENSG00000198133	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10130096	0.83[CEU][hapmap]
rs10133618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134444	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10143518	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873204	0.84[ASN][1000 genomes]
rs11158675	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158676	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11158677	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158678	0.84[ASN][1000 genomes]
rs11621977	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627207	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878949	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12878981	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12879556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12887115	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555398	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980614	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273596	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4899206	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902477	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573776	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs7140327	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140470	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144624	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154258	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7155830	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7155911	0.95[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7156144	0.95[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7160654	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160944	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8011307	0.83[ASN][1000 genomes]
rs8019176	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019974	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1320	chr14:67938724-67984157	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7161368	PPP2R5E	cis	cerebellum	SCAN
rs7161368	PLEKHG3	cis	cerebellum	SCAN
rs7161368	RDH11	cis	parietal	SCAN
rs7161368	SRSF5	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67982600-67984000	Enhancers	Primary B cells from peripheral blood	blood
2	chr14:67982600-67984000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr14:67982600-67984000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr14:67982600-67984000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr14:67982600-67984000	Enhancers	Brain Angular Gyrus	brain
6	chr14:67982600-67984000	Enhancers	Colon Smooth Muscle	Colon
7	chr14:67982600-67984000	Bivalent Enhancer	Placenta	Placenta
8	chr14:67982600-67999000	Weak transcription	Right Atrium	heart
9	chr14:67982800-67984000	Enhancers	Primary hematopoietic stem cells	blood
10	chr14:67982800-67984000	Enhancers	Brain Anterior Caudate	brain
11	chr14:67982800-67984000	Enhancers	Brain Cingulate Gyrus	brain
12	chr14:67982800-67984000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:67982800-67984200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr14:67982800-67984600	Enhancers	Primary B cells from cord blood	blood
15	chr14:67983000-67984000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr14:67983000-67984000	Bivalent Enhancer	HepG2	liver
17	chr14:67983000-67984200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr14:67983000-67985400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:67983000-67986200	Enhancers	Fetal Thymus	thymus
20	chr14:67983000-67987400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:67983400-67984000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
22	chr14:67983400-67984000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr14:67983400-67984200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr14:67983600-67984000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr14:67983600-67984400	Enhancers	Brain Substantia Nigra	brain
26	chr14:67983800-67984000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr14:67983800-67984000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:67983800-67984000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:67983800-67984000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr14:67983800-67984000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr14:67983800-67984000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr14:67983800-67984000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:67983800-67984000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
34	chr14:67983800-67984000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr14:67983800-67984000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:67983800-67984000	Enhancers	Liver	Liver
37	chr14:67983800-67984000	Bivalent Enhancer	Brain Germinal Matrix	brain
38	chr14:67983800-67984000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr14:67983800-67984000	Enhancers	Colonic Mucosa	Colon
40	chr14:67983800-67984000	Enhancers	Duodenum Mucosa	Duodenum
41	chr14:67983800-67984000	Enhancers	Fetal Brain Male	brain
42	chr14:67983800-67984000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr14:67983800-67984000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr14:67983800-67984000	Enhancers	Gastric	stomach
45	chr14:67983800-67984000	Enhancers	Pancreas	Pancrea
46	chr14:67983800-67984000	Enhancers	Right Ventricle	heart
47	chr14:67983800-67984000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr14:67983800-67984000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr14:67983800-67984000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr14:67983800-67984000	Enhancers	Spleen	Spleen

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