Variant report

Variant	rs1197660
Chromosome Location	chr15:42145936-42145937
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42145929-42146497	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:42143947-42146202	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:42143763-42146570	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr15:42140910-42146784	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42144528..42146188-chr15:42157927..42160220,2	K562	blood:
2	chr15:42129213..42131992-chr15:42145295..42147962,3	K562	blood:
3	chr15:42129367..42131992-chr15:42144303..42147962,3	K562	blood:
4	chr15:42145763..42147692-chr15:42149451..42151046,2	K562	blood:
5	chr15:42143417..42146188-chr15:42158720..42160287,2	K562	blood:

No data

Variant related genes	Relation type
SPTBN5	TF binding region
RNA5SP393	TF binding region
ENSG00000264850	Chromatin interaction
ENSG00000243708	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1122884	0.87[CEU][hapmap]
rs11634083	0.85[CEU][hapmap]
rs1197667	0.83[CEU][hapmap]
rs1197669	0.87[CEU][hapmap]
rs1197671	0.83[CEU][hapmap]
rs1197672	0.83[CEU][hapmap]
rs1197673	0.81[EUR][1000 genomes]
rs1197675	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1197703	0.87[CEU][hapmap]
rs1197705	0.83[CEU][hapmap]
rs2925339	0.83[CEU][hapmap]
rs890503	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs890506	0.93[ASN][1000 genomes]
rs890507	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	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
5	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816120	chr15:42093384-42171578	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
8	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
10	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	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
14	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
15	nsv904117	chr15:42103822-42184794	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
17	nsv904120	chr15:42109975-42153085	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv904121	chr15:42109975-42162957	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
19	nsv904122	chr15:42109975-42166475	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
20	nsv904123	chr15:42109975-42171483	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
21	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
22	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
23	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
24	nsv1050892	chr15:42128855-42186482	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
25	nsv904126	chr15:42132896-42171483	Enhancers Strong transcription Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
26	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
27	nsv904127	chr15:42142912-42207905	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1197660	SPTBN5	cis	Thyroid	GTEx
rs1197660	SPTBN5	cis	lung	GTEx
rs1197660	SPTBN5	cis	Artery Tibial	GTEx
rs1197660	SPTBN5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42121000-42147400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:42126200-42152400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:42131000-42162800	Weak transcription	HSMM	muscle
6	chr15:42136400-42146800	Weak transcription	Fetal Kidney	kidney
7	chr15:42138200-42173400	Weak transcription	Right Atrium	heart
8	chr15:42140400-42147800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42141000-42146400	Enhancers	Fetal Lung	lung
10	chr15:42141000-42147200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42141000-42147400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:42141000-42147600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:42141000-42149400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:42141000-42152200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:42141000-42154600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:42141200-42147000	Weak transcription	Fetal Thymus	thymus
17	chr15:42141200-42155200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
19	chr15:42141400-42152400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:42141400-42155800	Weak transcription	HSMMtube	muscle
21	chr15:42141600-42152200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:42141600-42152200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:42141600-42152200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:42141600-42152400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:42141600-42162600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:42141600-42163000	Weak transcription	Left Ventricle	heart
27	chr15:42141800-42147000	Weak transcription	Gastric	stomach
28	chr15:42141800-42152600	Weak transcription	Thymus	Thymus
29	chr15:42141800-42158200	Weak transcription	Liver	Liver
30	chr15:42142000-42152200	Weak transcription	Primary T cells from cord blood	blood
31	chr15:42142400-42146800	Weak transcription	Right Ventricle	heart
32	chr15:42142600-42155800	Weak transcription	Fetal Intestine Small	intestine
33	chr15:42143000-42159600	Weak transcription	HUVEC	blood vessel
34	chr15:42143600-42147400	Weak transcription	Spleen	Spleen
35	chr15:42143600-42165200	Weak transcription	Pancreas	Pancrea
36	chr15:42144400-42147000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:42144400-42147400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:42144400-42152400	Weak transcription	Lung	lung
39	chr15:42144600-42146200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr15:42144600-42149400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr15:42144800-42150800	Weak transcription	Esophagus	oesophagus
42	chr15:42145000-42146200	Bivalent Enhancer	Fetal Stomach	stomach
43	chr15:42145000-42147000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:42145200-42146000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr15:42145400-42146000	Weak transcription	Fetal Brain Female	brain
46	chr15:42145400-42146000	Enhancers	Placenta	Placenta
47	chr15:42145400-42146400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:42145400-42146600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:42145600-42146000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:42145600-42146200	Enhancers	Brain Inferior Temporal Lobe	brain

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