Variant report

Variant	rs9429486
Chromosome Location	chr1:113157372-113157373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:101)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:101 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:113157169-113157386	GM10248	blood:	n/a	n/a
2	RAD21	chr1:113157111-113157408	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:113157258-113157382	K562	blood:	n/a	n/a
4	CTCF	chr1:113157320-113157470	HFF-Myc	foreskin:	n/a	n/a
5	CTCF	chr1:113157240-113157390	GM12869	blood:	n/a	n/a
6	ZNF384	chr1:113157074-113157425	K562	blood:	n/a	n/a
7	CTCF	chr1:113157217-113157388	GM19238	blood:	n/a	n/a
8	RAD21	chr1:113156934-113157484	IMR90	lung:	n/a	n/a
9	CTCF	chr1:113157070-113157463	HCT-116	colon:	n/a	n/a
10	CHD1	chr1:113156949-113157443	IMR90	lung:	n/a	n/a
11	RAD21	chr1:113156941-113157610	HCT-116	colon:	n/a	n/a
12	CTCF	chr1:113157073-113157476	IMR90	lung:	n/a	n/a
13	CTCF	chr1:113157260-113157410	HCM	heart:	n/a	n/a
14	CTCF	chr1:113157234-113157395	MCF-7	breast:	n/a	n/a
15	CTCF	chr1:113157088-113157419	K562	blood:	n/a	n/a
16	ZMIZ1	chr1:113157139-113157381	K562	blood:	n/a	n/a
17	CTCF	chr1:113156867-113157588	A549	lung:	n/a	n/a
18	SMC3	chr1:113156748-113157524	SK-N-SH	brain:	n/a	n/a
19	SMC3	chr1:113157122-113157389	K562	blood:	n/a	n/a
20	ZNF143	chr1:113157185-113157385	K562	blood:	n/a	n/a
21	RAD21	chr1:113157118-113157396	GM12878	blood:	n/a	n/a
22	CTCF	chr1:113157226-113157387	GM12892	blood:	n/a	n/a
23	RAD21	chr1:113157042-113157453	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr1:113156978-113157476	A549	lung:	n/a	n/a
25	SMC3	chr1:113157160-113157411	HepG2	liver:	n/a	n/a
26	CTCF	chr1:113157240-113157390	GM12878	blood:	n/a	n/a
27	RAD21	chr1:113157130-113157397	A549	lung:	n/a	n/a
28	CTCF	chr1:113157091-113157415	HepG2	liver:	n/a	n/a
29	CTCF	chr1:113157139-113157388	Spleen_OC	spleen:	n/a	n/a
30	SMC3	chr1:113157057-113157449	GM12878	blood:	n/a	n/a
31	RAD21	chr1:113157011-113157480	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr1:113156876-113157594	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr1:113157067-113157471	GM12878	blood:	n/a	n/a
34	CTCF	chr1:113157225-113157388	A549	lung:	n/a	n/a
35	CTCF	chr1:113157085-113157441	A549	lung:	n/a	n/a
36	RAD21	chr1:113157070-113157447	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr1:113157009-113157538	MCF-7	breast:	n/a	n/a
38	CTCF	chr1:113157280-113157430	A549	lung:	n/a	n/a
39	CTCF	chr1:113157181-113157375	LNCaP	prostate:	n/a	n/a
40	CTCF	chr1:113157240-113157390	AG09319	gingival:	n/a	n/a
41	CTCF	chr1:113157058-113157383	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr1:113157156-113157389	K562	blood:	n/a	n/a
43	RAD21	chr1:113157059-113157413	K562	blood:	n/a	n/a
44	CTCF	chr1:113157240-113157390	HUVEC	blood vessel:	n/a	n/a
45	RAD21	chr1:113157044-113157516	MCF-7	breast:	n/a	n/a
46	RAD21	chr1:113157144-113157408	HepG2	liver:	n/a	n/a
47	CTCF	chr1:113157097-113157380	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr1:113157206-113157389	MCF-7	breast:	n/a	n/a
49	CTCF	chr1:113157078-113157444	K562	blood:	n/a	n/a
50	CTCF	chr1:113157214-113157394	GM19240	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113051289..113053628-chr1:113155844..113157474,2	MCF-7	breast:
2	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
3	chr1:113044125..113045114-chr1:113156151..113157755,13	MCF-7	breast:
4	chr1:113137197..113139930-chr1:113155526..113159416,3	MCF-7	breast:
5	chr1:112936501..112937762-chr1:113156864..113157564,3	K562	blood:
6	chr1:112933208..112934080-chr1:113156947..113157750,2	K562	blood:
7	chr1:112931259..112933878-chr1:113156941..113159026,2	K562	blood:
8	chr1:112931958..112934579-chr1:113156530..113159050,3	MCF-7	breast:
9	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
10	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
11	chr1:112934954..112937732-chr1:113156801..113159593,3	MCF-7	breast:
12	chr1:112932849..112934101-chr1:113156867..113157927,5	MCF-7	breast:
13	chr1:112933554..112934212-chr1:113157017..113157740,2	MCF-7	breast:
14	chr1:113155240..113157847-chr1:113166042..113168609,2	K562	blood:
15	chr1:113008918..113009447-chr1:113157082..113157668,2	K562	blood:
16	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
17	chr1:113155822..113159612-chr1:113243591..113247554,4	K562	blood:
18	chr1:113004968..113007930-chr1:113157239..113158871,3	MCF-7	breast:

No data

Variant related genes	Relation type
CAPZA1	TF binding region
ST7L	TF binding region
ENSG00000134245	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000143079	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10745330	0.89[CEU][hapmap]
rs10776755	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs10776757	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857963	0.89[CEU][hapmap]
rs1110043	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs11584092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12042407	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12046208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126277	0.89[CEU][hapmap]
rs12728001	0.86[CEU][hapmap]
rs1994604	0.81[EUR][1000 genomes]
rs2932532	0.89[CEU][hapmap]
rs2932536	0.88[CEU][hapmap]
rs2999154	0.85[CEU][hapmap]
rs2999155	0.89[CEU][hapmap]
rs3013439	0.88[CEU][hapmap]
rs3013440	0.89[CEU][hapmap]
rs351372	0.85[CEU][hapmap]
rs4838959	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs4839254	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs507213	0.80[EUR][1000 genomes]
rs55675817	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537748	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6537749	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs663533	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666579	0.89[CEU][hapmap]
rs6682737	0.89[CEU][hapmap]
rs6700673	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs72699100	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7415820	0.89[CEU][hapmap]
rs7512948	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7513716	0.89[CEU][hapmap]
rs7522288	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544663	0.88[CEU][hapmap]
rs7546094	0.81[EUR][1000 genomes]
rs7554916	0.85[CEU][hapmap]
rs902289	0.88[CEU][hapmap]
rs910697	0.85[CEU][hapmap]
rs937053	0.84[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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer 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	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9429486	ST7L	cis	Adipose Subcutaneous	GTEx
rs9429486	ST7L	cis	multi-tissue	Pritchard
rs9429486	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs9429486	ST7L	cis	lesional skin	skin_eQTL
rs9429486	ST7L	cis	uninvolved skin	skin_eQTL
rs9429486	ST7L	cis	normal skin	skin_eQTL
rs9429486	ST7L	cis	lung	GTEx
rs9429486	ST7L	cis	Nerve Tibial	GTEx
rs9429486	ST7L	cis	Thyroid	GTEx
rs9429486	ST7L	cis	Lymphoblastoid	GTEx
rs9429486	ST7L	cis	Esophagus Muscularis	GTEx
rs9429486	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs9429486	ST7L	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113109000-113160000	Weak transcription	Gastric	stomach
2	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
3	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
4	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
8	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
10	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
18	chr1:113139200-113159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:113140200-113159200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:113140600-113159200	Strong transcription	Fetal Stomach	stomach
22	chr1:113144000-113158600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:113145000-113159600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:113145800-113159400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:113146800-113159000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:113147800-113158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:113148200-113158400	Strong transcription	Brain Germinal Matrix	brain
29	chr1:113148200-113158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:113148200-113158800	Strong transcription	Liver	Liver
31	chr1:113148200-113158800	Strong transcription	Dnd41	blood
32	chr1:113148200-113159000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:113148200-113159000	Strong transcription	Placenta	Placenta
34	chr1:113148200-113159200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:113148200-113159800	Strong transcription	Fetal Intestine Small	intestine
36	chr1:113148400-113158600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:113148400-113158600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:113148400-113158800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:113148400-113158800	Strong transcription	Adipose Nuclei	Adipose
40	chr1:113148400-113158800	Strong transcription	Osteobl	bone
41	chr1:113148400-113159000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:113148400-113159200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:113148400-113159200	Strong transcription	Fetal Brain Female	brain
44	chr1:113148400-113159200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:113148600-113159000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:113148600-113159200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:113148800-113158400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:113148800-113158800	Strong transcription	Hela-S3	cervix
49	chr1:113148800-113159000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:113148800-113159200	Strong transcription	Fetal Thymus	thymus

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