Variant report

Variant	rs1704386
Chromosome Location	chr15:42197483-42197484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42176708..42178291-chr15:42195146..42197616,2	K562	blood:
2	chr15:42184589..42187118-chr15:42195366..42198157,2	K562	blood:
3	chr15:42114988..42115997-chr15:42196197..42197506,6	MCF-7	breast:
4	chr15:42196907..42199684-chr15:42201909..42205293,3	K562	blood:
5	chr15:42180442..42182824-chr15:42195792..42198246,2	K562	blood:

Variant related genes	Relation type
ENSG00000174171	Chromatin interaction
ENSG00000137877	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1048166	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1048175	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1113333	0.84[AFR][1000 genomes]
rs1648810	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648815	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648818	0.80[ASN][1000 genomes]
rs1704381	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704388	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704391	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704396	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820506	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28547280	0.80[ASN][1000 genomes]
rs6493011	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7183264	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041458	0.80[ASN][1000 genomes]
rs890502	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv904128	chr15:42147639-42207905	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
13	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
14	nsv904129	chr15:42162957-42207905	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1704386	SPTBN5	cis	Esophagus Muscularis	GTEx
rs1704386	SPTBN5	cis	Whole Blood	GTEx
rs1704386	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs1704386	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs1704386	SPTBN5	cis	lung	GTEx
rs1704386	SPTBN5	cis	Artery Aorta	GTEx
rs1704386	SPTBN5	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42186800-42198800	Weak transcription	Brain Substantia Nigra	brain
2	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
3	chr15:42187600-42198800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:42187600-42200400	Weak transcription	Stomach Mucosa	stomach
5	chr15:42187600-42200600	Weak transcription	HepG2	liver
6	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:42187800-42198000	Strong transcription	Fetal Intestine Small	intestine
8	chr15:42187800-42206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42188000-42198600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:42188000-42198800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:42188600-42209600	Strong transcription	NHEK	skin
12	chr15:42189000-42198200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:42189400-42198800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:42189800-42208400	Strong transcription	HUVEC	blood vessel
15	chr15:42190200-42209800	Weak transcription	Hela-S3	cervix
16	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
17	chr15:42191600-42198600	Weak transcription	Osteobl	bone
18	chr15:42192200-42198000	Enhancers	Fetal Heart	heart
19	chr15:42192400-42198600	Weak transcription	Ovary	ovary
20	chr15:42192600-42197800	Weak transcription	Primary T cells from cord blood	blood
21	chr15:42192600-42204000	Strong transcription	Esophagus	oesophagus
22	chr15:42193200-42198200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:42193200-42199000	Weak transcription	NH-A	brain
24	chr15:42193400-42198600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:42193400-42200600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:42193600-42198000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:42193600-42198200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:42193600-42198200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:42193600-42198400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:42193600-42198600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:42193600-42200600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:42193800-42198000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:42193800-42198600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:42193800-42198600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:42194200-42198800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:42194400-42198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:42194400-42198200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:42194400-42198200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:42194600-42197800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:42194600-42198000	Weak transcription	Gastric	stomach
41	chr15:42194600-42198600	Weak transcription	Pancreas	Pancrea
42	chr15:42195400-42198400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:42195400-42200600	Weak transcription	NHDF-Ad	bronchial
44	chr15:42195800-42197800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr15:42195800-42197800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:42195800-42198200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:42195800-42198400	Genic enhancers	Fetal Muscle Leg	muscle
48	chr15:42195800-42199400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:42195800-42209000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:42196000-42197600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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