Variant report

Variant	rs11102514
Chromosome Location	chr1:113160419-113160420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:113160214-113163630	K562	blood:	n/a	n/a
2	POLR2A	chr1:113160211-113163888	IMR90	lung:	n/a	n/a
3	CHD1	chr1:113160361-113165418	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:113160415-113163657	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr1:113160220-113163715	SK-N-SH	brain:	n/a	n/a
6	CBX3	chr1:113159922-113160448	K562	blood:	n/a	n/a
7	POLR2A	chr1:113160236-113163811	SK-N-MC	brain:	n/a	n/a
8	HCFC1	chr1:113160269-113163626	Hela-S3	cervix:	n/a	n/a
9	JUN	chr1:113160308-113164479	K562	blood:	n/a	n/a
10	POLR2A	chr1:113160298-113163460	PBDE	blood:	n/a	n/a
11	RUNX3	chr1:113160273-113161436	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:113160266-113160624	HepG2	liver:	n/a	n/a

No data

(count:18 , 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	chr1:113160176..113163931-chr1:113238020..113242018,6	K562	blood:
4	chr1:113160312..113164959-chr1:113166253..113170624,10	MCF-7	breast:
5	chr1:113002255..113010411-chr1:113160144..113164475,13	MCF-7	breast:
6	chr1:113159954..113164373-chr1:113192711..113196451,4	K562	blood:
7	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
8	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
9	chr1:113003059..113010084-chr1:113159503..113164005,9	MCF-7	breast:
10	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
11	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
12	chr1:113059419..113061818-chr1:113160250..113161994,2	MCF-7	breast:
13	chr1:113160231..113165111-chr1:113199772..113204361,6	K562	blood:
14	chr1:113050070..113052532-chr1:113159337..113161675,2	MCF-7	breast:
15	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
16	chr1:113160402..113162739-chr1:113234192..113237024,2	K562	blood:
17	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
18	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
ENSG00000143079	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000273483	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

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	0.82[CHB][hapmap];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]
rs11102513	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	0.91[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];0.95[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];0.95[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];1.00[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];1.00[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];0.95[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];1.00[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];0.91[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];0.91[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]
rs3790606	0.82[CHB][hapmap]
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
rs11102514	ST7L	cis	multi-tissue	Pritchard
rs11102514	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs11102514	ST7L	cis	Lymphoblastoid	GTEx
rs11102514	ST7L	cis	normal skin	skin_eQTL

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	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:113148800-113160800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:113150200-113160800	Weak transcription	Aorta	Aorta
6	chr1:113153400-113160600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:113153600-113160600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:113155000-113161000	Weak transcription	Esophagus	oesophagus
9	chr1:113158200-113160600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:113158600-113160600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:113158800-113160600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:113159000-113161000	Weak transcription	Placenta	Placenta
13	chr1:113159000-113161200	Weak transcription	Ovary	ovary
14	chr1:113159400-113160800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:113159800-113160600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:113159800-113160600	Enhancers	Liver	Liver
17	chr1:113159800-113160600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:113159800-113160600	Flanking Active TSS	GM12878-XiMat	blood
19	chr1:113159800-113160800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:113159800-113160800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr1:113159800-113160800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:113159800-113161000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:113159800-113161000	Flanking Active TSS	Dnd41	blood
24	chr1:113159800-113161400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr1:113159800-113164000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:113160000-113160600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:113160000-113160600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:113160000-113160600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr1:113160000-113160600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr1:113160000-113160600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr1:113160000-113160600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:113160000-113160600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:113160000-113160600	Enhancers	Adipose Nuclei	Adipose
34	chr1:113160000-113160600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:113160000-113160600	Enhancers	Fetal Intestine Large	intestine
36	chr1:113160000-113160600	Enhancers	Fetal Muscle Leg	muscle
37	chr1:113160000-113160600	Enhancers	Fetal Stomach	stomach
38	chr1:113160000-113160600	Enhancers	Fetal Thymus	thymus
39	chr1:113160000-113160600	Enhancers	Left Ventricle	heart
40	chr1:113160000-113160600	Enhancers	Lung	lung
41	chr1:113160000-113160600	Enhancers	Pancreas	Pancrea
42	chr1:113160000-113160600	Enhancers	Rectal Smooth Muscle	rectum
43	chr1:113160000-113160600	Enhancers	Right Ventricle	heart
44	chr1:113160000-113160600	Enhancers	Stomach Mucosa	stomach
45	chr1:113160000-113160800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:113160000-113160800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr1:113160000-113160800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:113160000-113160800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:113160000-113160800	Enhancers	Fetal Heart	heart
50	chr1:113160000-113160800	Flanking Active TSS	HUVEC	blood vessel

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