Variant report

Variant	rs1704396
Chromosome Location	chr15:42211486-42211487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42210672-42212000	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:42209758-42212774	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:42210611-42212076	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:42209786-42212072	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:42210650-42212167	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:42209705-42212218	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:42210630-42212143	GM12891	blood:	n/a	n/a
8	POLR2A	chr15:42211334-42211929	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:42210704-42212101	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:42210847-42211517	GM12892	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42211437-42211487	MCF10A-Er-Src	breast:	n/a
2	chr15:42211437-42211487	T-47D	breast:	n/a
3	chr15:42211437-42211487	U87	brain:	n/a
4	chr15:42211437-42211487	RPTEC	kidney:	n/a
5	chr15:42211437-42211487	SKMC	muscle:	n/a
6	chr15:42211437-42211487	HepG2	liver:	n/a
7	chr15:42211437-42211487	K562	blood:	n/a
8	chr15:42211437-42211487	NHDF-neo	bronchial:	n/a
9	chr15:42211437-42211487	Caco-2	colon:	n/a
10	chr15:42211437-42211487	HEEpiC	esophagus:	n/a
11	chr15:42211437-42211487	HCF	heart:	n/a
12	chr15:42211437-42211487	HRCEpiC	kidney:	n/a
13	chr15:42211437-42211487	IMR90	lung:	fetal
14	chr15:42211437-42211487	GM12878	blood:	n/a
15	chr15:42211437-42211487	MCF-7	breast:	n/a
16	chr15:42211437-42211487	SK-N-SH	brain:	n/a
17	chr15:42211437-42211487	PrEC	prostate:	n/a
18	chr15:42211437-42211487	ovcar-3	ovarian:	n/a
19	chr15:42211437-42211487	HUVEC	blood vessel:	n/a
20	chr15:42211437-42211487	AG04449	skin:	fetal
21	chr15:42211437-42211487	BJ	skin:	n/a
22	chr15:42211437-42211487	GM19239	blood:	n/a
23	chr15:42211437-42211487	HCT-116	colon:	n/a
24	chr15:42211437-42211487	HCPEpiC	choroid plexus:	n/a
25	chr15:42211437-42211487	GM06990	blood:	n/a
26	chr15:42211437-42211487	ECC-1	luminal epithelium:	n/a
27	chr15:42211437-42211487	GM12891	blood:	n/a
28	chr15:42211437-42211487	BE2_C	brain:	n/a
29	chr15:42211437-42211487	ProgFib	skin:	n/a
30	chr15:42211437-42211487	CMK	blood:	n/a
31	chr15:42211437-42211487	HRE	kidney:	n/a
32	chr15:42211437-42211487	AoSMC	blood vessel:	n/a
33	chr15:42211437-42211487	SAEC	small airway:	n/a
34	chr15:42211437-42211487	AG09319	gingival:	n/a
35	chr15:42211437-42211487	SK-N-MC	brain:	n/a
36	chr15:42211437-42211487	HCM	heart:	n/a
37	chr15:42211437-42211487	GM12892	blood:	n/a
38	chr15:42211437-42211487	NH-A	brain:	n/a
39	chr15:42211437-42211487	PFSK-1	brain:	n/a
40	chr15:42211437-42211487	HEK293	kidney:	embryo
41	chr15:42211437-42211487	H1-hESC	embryonic stem cell:	embryo
42	chr15:42211437-42211487	NT2-D1	testis:	n/a
43	chr15:42211437-42211487	HPAEpiC	pulmonary alveolar:	n/a
44	chr15:42211437-42211487	Hepatocyte	liver:	n/a
45	chr15:42211437-42211487	PANC-1	pancreas:	n/a
46	chr15:42211437-42211487	Jurkat	blood:	n/a
47	chr15:42211437-42211487	HIPEpiC	eye:	n/a
48	chr15:42211437-42211487	LNCaP	prostate:	n/a
49	chr15:42211437-42211487	HNPCEpiC	eye:	n/a
50	chr15:42211437-42211487	AG10803	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42200852..42203519-chr15:42209900..42211491,2	K562	blood:
2	chr15:42209684..42211751-chr15:42216402..42218970,2	MCF-7	breast:
3	chr15:42202438..42205069-chr15:42210826..42212891,2	MCF-7	breast:
4	chr15:42207550..42209850-chr15:42209914..42212582,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259883	TF binding region
ENSG00000259883	CpG island

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1048166	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1048175	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10518741	0.85[CHB][hapmap]
rs1197691	0.85[CHB][hapmap]
rs1209334	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs1648810	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648815	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648818	0.80[ASN][1000 genomes]
rs1672461	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs1704381	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704386	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704388	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704391	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704392	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs17686769	0.83[CHD][hapmap]
rs1820506	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28547280	0.80[ASN][1000 genomes]
rs6493011	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7183264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041458	0.80[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs890502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
5	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
6	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
7	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv976926	chr15:42202094-42217599	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1704396	SPTBN5	cis	lung	GTEx
rs1704396	SPTBN5	cis	Esophagus Muscularis	GTEx
rs1704396	SPTBN5	cis	Artery Tibial	GTEx
rs1704396	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs1704396	SPTBN5	cis	Artery Aorta	GTEx
rs1704396	SPTBN5	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
2	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
3	chr15:42197200-42218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:42197400-42218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:42198200-42212000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:42198800-42212000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr15:42199000-42212600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:42201200-42225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42201800-42211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:42202200-42218400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:42202200-42218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:42202200-42225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:42204000-42217600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:42204200-42212000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:42208200-42212000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:42208200-42212000	Strong transcription	Primary T cells from cord blood	blood
17	chr15:42208200-42212000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:42208200-42212000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:42208400-42212000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:42208400-42212000	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr15:42208400-42212000	Genic enhancers	Fetal Muscle Leg	muscle
22	chr15:42208400-42212000	Genic enhancers	Lung	lung
23	chr15:42208400-42212800	Genic enhancers	Placenta	Placenta
24	chr15:42208400-42214400	Enhancers	Right Atrium	heart
25	chr15:42208400-42214800	Enhancers	Ovary	ovary
26	chr15:42208400-42218800	Genic enhancers	HUVEC	blood vessel
27	chr15:42208600-42211800	Weak transcription	Fetal Kidney	kidney
28	chr15:42208800-42211800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:42209200-42212000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:42209200-42218000	Weak transcription	Fetal Thymus	thymus
31	chr15:42209600-42213800	Genic enhancers	Fetal Intestine Small	intestine
32	chr15:42209800-42211600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:42209800-42211600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:42209800-42211600	Genic enhancers	Left Ventricle	heart
35	chr15:42209800-42211800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr15:42209800-42211800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:42209800-42211800	Transcr. at gene 5' and 3'	Pancreas	Pancrea
38	chr15:42209800-42211800	Enhancers	Psoas Muscle	Psoas
39	chr15:42209800-42212000	Genic enhancers	NHLF	lung
40	chr15:42209800-42212400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:42209800-42212800	Genic enhancers	Spleen	Spleen
42	chr15:42209800-42216000	Strong transcription	GM12878-XiMat	blood
43	chr15:42210000-42211800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:42210000-42211800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:42210000-42211800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr15:42210000-42212000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:42210000-42212000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:42210000-42212000	Strong transcription	Colonic Mucosa	Colon
49	chr15:42210000-42212000	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr15:42210000-42212000	Genic enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links