Variant report

Variant	rs7522288
Chromosome Location	chr1:113151205-113151206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113143618..113146588-chr1:113149750..113152817,3	K562	blood:
2	chr1:113148930..113152867-chr1:113160245..113163923,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10745330	0.82[CEU][hapmap]
rs10776755	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs10776757	0.93[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857963	0.82[CEU][hapmap]
rs1110043	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11584092	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12042407	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12046208	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126277	0.82[CEU][hapmap]
rs2932532	0.82[CEU][hapmap]
rs2932536	0.81[CEU][hapmap]
rs2999155	0.82[CEU][hapmap]
rs3013439	0.81[CEU][hapmap]
rs3013440	0.82[CEU][hapmap]
rs4838959	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4839254	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55675817	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537748	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6537749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs663533	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666579	0.82[CEU][hapmap]
rs6682737	0.82[CEU][hapmap]
rs6700673	0.81[CEU][hapmap]
rs72699100	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7415820	0.82[CEU][hapmap]
rs7512948	0.85[EUR][1000 genomes]
rs7513716	0.82[CEU][hapmap]
rs7544663	0.81[CEU][hapmap]
rs902289	0.81[CEU][hapmap]
rs937053	0.84[ASN][1000 genomes]
rs9429486	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]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7522288	ST7L	cis	lesional skin	skin_eQTL
rs7522288	ST7L	cis	Thyroid	GTEx
rs7522288	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs7522288	ST7L	cis	Artery Tibial	GTEx
rs7522288	ST7L	cis	lung	GTEx
rs7522288	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs7522288	ST7L	cis	normal skin	skin_eQTL
rs7522288	ST7L	cis	uninvolved skin	skin_eQTL
rs7522288	ST7L	cis	multi-tissue	Pritchard

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	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
4	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
5	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
6	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
10	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
11	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:113133000-113152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:113133000-113152400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
16	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:113136200-113156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:113137000-113154200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:113139200-113159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:113140200-113152600	Weak transcription	Primary B cells from cord blood	blood
28	chr1:113140200-113159200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:113140600-113159200	Strong transcription	Fetal Stomach	stomach
31	chr1:113144000-113158600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:113145000-113159600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:113145800-113159400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:113146200-113156000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:113146400-113151400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:113146400-113152800	Weak transcription	Fetal Kidney	kidney
38	chr1:113146800-113159000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:113147800-113158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:113148200-113151800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr1:113148200-113153600	Strong transcription	Left Ventricle	heart
42	chr1:113148200-113154000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:113148200-113156600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:113148200-113156800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:113148200-113156800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:113148200-113158400	Strong transcription	Brain Germinal Matrix	brain
47	chr1:113148200-113158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:113148200-113158800	Strong transcription	Liver	Liver
49	chr1:113148200-113158800	Strong transcription	Dnd41	blood
50	chr1:113148200-113159000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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