Variant report

Variant	rs4838961
Chromosome Location	chr1:113163967-113163968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
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	ZNF384	chr1:113163643-113165679	GM12878	blood:	n/a	n/a
2	CHD1	chr1:113160361-113165418	GM12878	blood:	n/a	n/a
3	ELF1	chr1:113163868-113164175	GM12878	blood:	n/a	chr1:113163952-113163965
4	ZNF384	chr1:113163555-113164124	K562	blood:	n/a	n/a
5	POLR2A	chr1:113163954-113164137	HepG2	liver:	n/a	n/a
6	JUN	chr1:113160308-113164479	K562	blood:	n/a	n/a
7	ELF1	chr1:113163769-113164176	K562	blood:	n/a	chr1:113163952-113163965
8	POLR2A	chr1:113163881-113164098	GM12878	blood:	n/a	n/a
9	CHD1	chr1:113160459-113163971	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:113163838-113164271	GM12892	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:112934882..112939118-chr1:113160574..113165273,5	K562	blood:
2	chr1:113161978..113164385-chr9:33816477..33818971,2	MCF-7	breast:
3	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
4	chr1:113163032..113164854-chr1:113235920..113238010,2	K562	blood:
5	chr1:113160443..113165363-chr1:113242054..113245654,5	K562	blood:
6	chr1:113160312..113164959-chr1:113166253..113170624,10	MCF-7	breast:
7	chr1:113002255..113010411-chr1:113160144..113164475,13	MCF-7	breast:
8	chr1:113159954..113164373-chr1:113192711..113196451,4	K562	blood:
9	chr1:113160723..113165170-chr1:113245654..113250392,12	K562	blood:
10	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
11	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
12	chr1:113003059..113010084-chr1:113159503..113164005,9	MCF-7	breast:
13	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
14	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
15	chr1:113162339..113164666-chr17:59475031..59477488,2	MCF-7	breast:
16	chr1:113160231..113165111-chr1:113199772..113204361,6	K562	blood:
17	chr1:113160638..113164364-chr1:113256565..113260015,7	MCF-7	breast:
18	chr1:113160723..113165186-chr1:113170921..113177730,6	MCF-7	breast:
19	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
20	chr1:113160799..113166409-chr1:113215716..113220433,9	K562	blood:
21	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
22	chr1:113160555..113166228-chr1:113255932..113262161,8	K562	blood:

No data

Variant related genes	Relation type
ST7L	TF binding region
ENSG00000261595	Chromatin interaction
ENSG00000252750	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000107341	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000235481	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000143079	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10745332	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857969	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102494	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11102508	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102510	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11102517	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12048528	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12118370	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119489	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12125361	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12126494	0.84[EUR][1000 genomes]
rs12136781	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12137107	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138335	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143068	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1238	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12401734	0.81[EUR][1000 genomes]
rs12402469	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12402929	0.81[EUR][1000 genomes]
rs12406906	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12739994	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12750023	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12750621	0.84[EUR][1000 genomes]
rs12758377	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17438324	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273369	0.81[EUR][1000 genomes]
rs2932529	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2932534	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932535	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932538	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2932539	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3013433	0.80[EUR][1000 genomes]
rs3013441	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34531155	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35482634	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36029940	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3762335	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3790611	0.80[EUR][1000 genomes]
rs3790612	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3795820	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4240534	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838960	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839257	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61818772	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61818800	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537740	0.83[EUR][1000 genomes]
rs6537744	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6537745	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537747	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6658555	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6659677	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6661642	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6663922	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668533	0.80[EUR][1000 genomes]
rs6671645	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6672761	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6673930	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674053	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674068	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681371	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6682678	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6690169	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6690292	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6691025	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691917	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693880	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696991	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698030	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6701351	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7415988	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7512984	0.81[EUR][1000 genomes]
rs7516421	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519368	0.89[EUR][1000 genomes]
rs7522110	0.81[EUR][1000 genomes]
rs7527076	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535636	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7537789	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7542820	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7546203	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7549547	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7551933	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7552692	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9429694	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662162	0.81[AMR][1000 genomes]
rs999923	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4838961	ST7L	cis	lung	GTEx
rs4838961	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113159800-113164000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:113160000-113164400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:113160000-113165400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:113160400-113164000	Active TSS	Psoas Muscle	Psoas
5	chr1:113160400-113164000	Active TSS	A549	lung
6	chr1:113160400-113164600	Active TSS	K562	blood
7	chr1:113160600-113166000	Active TSS	GM12878-XiMat	blood
8	chr1:113161000-113164000	Active TSS	NHLF	lung
9	chr1:113161400-113164200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:113161800-113165400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:113162000-113164200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:113162600-113165000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr1:113162600-113165600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr1:113162800-113164800	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr1:113162800-113165200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:113162800-113165600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr1:113163000-113164000	Flanking Active TSS	Liver	Liver
18	chr1:113163000-113164000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:113163000-113164000	Weak transcription	Spleen	Spleen
20	chr1:113163000-113164200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:113163000-113164200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:113163000-113164400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:113163000-113165200	Flanking Active TSS	Dnd41	blood
24	chr1:113163000-113165400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:113163200-113164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:113163200-113164000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr1:113163200-113164000	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr1:113163200-113164000	Weak transcription	Lung	lung
29	chr1:113163200-113164000	Flanking Active TSS	Osteobl	bone
30	chr1:113163200-113164200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:113163200-113164200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:113163200-113164200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr1:113163200-113164400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:113163200-113164800	Flanking Active TSS	Hela-S3	cervix
35	chr1:113163200-113165000	Flanking Active TSS	HMEC	breast
36	chr1:113163200-113165400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:113163200-113165400	Flanking Active TSS	HUVEC	blood vessel
38	chr1:113163200-113165800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:113163200-113167400	Weak transcription	Small Intestine	intestine
40	chr1:113163200-113167600	Weak transcription	Gastric	stomach
41	chr1:113163200-113168400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:113163200-113168400	Weak transcription	Pancreas	Pancrea
43	chr1:113163400-113164000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:113163400-113164000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:113163400-113164000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr1:113163400-113164000	Flanking Active TSS	HepG2	liver
47	chr1:113163400-113164000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr1:113163400-113164200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:113163400-113164200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:113163400-113164200	Flanking Active TSS	Thymus	Thymus

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