Variant report

Variant	rs11102513
Chromosome Location	chr1:113160170-113160171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113160154-113160217	HepG2	liver:	n/a	n/a
2	CBX3	chr1:113159922-113160448	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113006478..113010487-chr1:113159582..113162671,3	K562	blood:
2	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
3	chr1:113002255..113010411-chr1:113160144..113164475,13	MCF-7	breast:
4	chr1:113159954..113164373-chr1:113192711..113196451,4	K562	blood:
5	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
6	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
7	chr1:113003059..113010084-chr1:113159503..113164005,9	MCF-7	breast:
8	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
9	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
10	chr1:113050070..113052532-chr1:113159337..113161675,2	MCF-7	breast:
11	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
12	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
13	chr1:113158960..113161878-chr1:113209000..113211428,3	MCF-7	breast:

No data

Variant related genes	Relation type
ST7L	TF binding region
CAPZA1	TF binding region
ENSG00000155366	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10857961	0.97[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10857964	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10857967	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1106287	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1110042	0.87[EUR][1000 genomes]
rs11102496	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102498	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11102501	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102509	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11102514	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102520	0.87[EUR][1000 genomes]
rs11102522	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs12029985	0.97[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12030612	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12030641	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12040988	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045227	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049572	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12117479	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12120956	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12122980	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126684	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12126971	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12130243	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12133583	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12137269	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12140506	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12406282	0.87[EUR][1000 genomes]
rs12406530	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12724928	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12728311	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12756815	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17030613	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17030651	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2009056	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064711	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273368	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2279499	0.83[ASN][1000 genomes]
rs2306937	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306940	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2887882	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34107138	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34569066	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34848593	0.87[EUR][1000 genomes]
rs35023236	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35147679	0.97[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3737136	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs3748656	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs3795819	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs55652172	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56135413	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs60900293	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61818802	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61818805	0.87[EUR][1000 genomes]
rs6679	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7522283	0.95[JPT][hapmap]
rs883593	0.87[EUR][1000 genomes]
rs9308256	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11102513	ST7L	cis	Lymphoblastoid	GTEx
rs11102513	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs11102513	ST7L	cis	normal skin	skin_eQTL
rs11102513	ST7L	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:113148800-113160800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:113150200-113160800	Weak transcription	Aorta	Aorta
9	chr1:113153400-113160200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:113153400-113160600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:113153600-113160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:113153600-113160600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:113154200-113160400	Weak transcription	A549	lung
14	chr1:113155000-113161000	Weak transcription	Esophagus	oesophagus
15	chr1:113156000-113160200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:113156000-113160400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:113156600-113160200	Weak transcription	NH-A	brain
18	chr1:113156800-113160200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:113156800-113160400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:113156800-113160400	Weak transcription	HSMMtube	muscle
21	chr1:113157200-113160200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:113158200-113160200	Weak transcription	K562	blood
23	chr1:113158200-113160600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:113158600-113160200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:113158600-113160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:113158600-113160400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:113158600-113160400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:113158600-113160600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:113158800-113160400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:113158800-113160600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:113159000-113160200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:113159000-113161000	Weak transcription	Placenta	Placenta
33	chr1:113159000-113161200	Weak transcription	Ovary	ovary
34	chr1:113159200-113160200	Weak transcription	Fetal Brain Female	brain
35	chr1:113159200-113160400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:113159200-113160400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:113159400-113160200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:113159400-113160800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:113159800-113160200	Enhancers	Primary T cells from cord blood	blood
40	chr1:113159800-113160200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:113159800-113160200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:113159800-113160200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:113159800-113160200	Enhancers	HepG2	liver
44	chr1:113159800-113160400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:113159800-113160400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:113159800-113160400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:113159800-113160400	Enhancers	Primary B cells from cord blood	blood
48	chr1:113159800-113160400	Enhancers	Brain Germinal Matrix	brain
49	chr1:113159800-113160400	Enhancers	HMEC	breast
50	chr1:113159800-113160400	Enhancers	Monocytes-CD14+_RO01746	blood

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