Variant report

Variant	rs7516421
Chromosome Location	chr1:113089696-113089697
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	chr1:113086848..113091301-chr1:113248595..113251395,3	MCF-7	breast:
2	chr1:113089513..113091265-chr1:113093037..113094577,2	K562	blood:

Variant related genes	Relation type
ENSG00000155366	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10745332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10857963	0.81[YRI][hapmap]
rs10857969	0.85[ASN][1000 genomes]
rs11102494	0.96[EUR][1000 genomes]
rs11102508	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102510	0.86[EUR][1000 genomes]
rs11102517	0.84[EUR][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12118370	0.87[ASN][1000 genomes]
rs12119489	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12136781	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137107	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12143068	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1238	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12401734	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12402469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402929	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs12406906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12739994	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12750023	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap]
rs12758377	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17438324	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932529	1.00[CEU][hapmap]
rs2932534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2932538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932539	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3013441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34531155	0.87[EUR][1000 genomes]
rs35482634	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36029940	0.96[EUR][1000 genomes]
rs3762335	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795820	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4240534	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4838960	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4838961	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs61818772	0.96[EUR][1000 genomes]
rs61818800	0.91[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6537742	0.84[CEU][hapmap]
rs6537744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6537747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6659677	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6661642	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6671645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672761	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674053	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674068	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6682678	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs6690169	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs6691025	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691917	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6693880	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698030	0.87[EUR][1000 genomes]
rs6701351	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7513716	0.81[YRI][hapmap]
rs7522110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7537789	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540251	0.86[EUR][1000 genomes]
rs7542820	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7546203	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549547	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552692	0.81[ASN][1000 genomes]
rs9429694	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs999923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7516421	ST7L	cis	multi-tissue	Pritchard
rs7516421	ST7L	cis	Nerve Tibial	GTEx
rs7516421	ST7L	cis	lung	GTEx
rs7516421	ST7L	cis	Lymphoblastoid	GTEx
rs7516421	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:113058800-113119400	Weak transcription	HepG2	liver
3	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
4	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
5	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
9	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
10	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:113066200-113114400	Weak transcription	Dnd41	blood
13	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
14	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
16	chr1:113070400-113095400	Weak transcription	Gastric	stomach
17	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
18	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:113070600-113117800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
24	chr1:113071200-113090600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:113072000-113114400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:113076400-113115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:113078800-113090200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:113080200-113117800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:113080800-113117400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
31	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:113082000-113106600	Weak transcription	Fetal Kidney	kidney
34	chr1:113082000-113116000	Weak transcription	Left Ventricle	heart
35	chr1:113082000-113117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:113082200-113118000	Weak transcription	Lung	lung
37	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
38	chr1:113083600-113091000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:113083600-113111600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:113083600-113114400	Weak transcription	Fetal Brain Female	brain
41	chr1:113083600-113117400	Weak transcription	Brain Angular Gyrus	brain
42	chr1:113084000-113114600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:113084200-113090600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:113084200-113091000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:113084200-113104400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:113084200-113110200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:113084200-113114800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:113084200-113117400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:113084200-113117400	Weak transcription	Brain Germinal Matrix	brain

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