Variant report

Variant	rs7415988
Chromosome Location	chr1:113159730-113159731
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 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	chr1:112939070..112940580-chr1:113158332..113159844,2	K562	blood:
4	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
5	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
6	chr1:113003059..113010084-chr1:113159503..113164005,9	MCF-7	breast:
7	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
8	chr1:113157493..113160120-chr1:113249713..113252199,3	K562	blood:
9	chr1:113050070..113052532-chr1:113159337..113161675,2	MCF-7	breast:
10	chr1:113157945..113159730-chr1:113240824..113243096,2	K562	blood:
11	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
12	chr1:113158960..113161878-chr1:113209000..113211428,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOC-3	chr1:113159435-113159908	NONHSAT005257

No data

Variant related genes	Relation type
ENSG00000134245	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap]
rs10745332	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10857969	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11102494	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11102508	0.93[EUR][1000 genomes]
rs11102510	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102517	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12118370	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12119489	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12125361	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12126494	0.84[EUR][1000 genomes]
rs12136781	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12137107	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12138335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143068	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12144044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1238	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12401734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12402469	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12402929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12406906	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12739994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750023	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12750621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12758377	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17438324	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2273369	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2279500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932534	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2932535	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2932537	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932538	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2932539	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3013433	0.80[EUR][1000 genomes]
rs3013441	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34531155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35482634	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36029940	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762335	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3790611	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3790612	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3795820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240534	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4838960	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4838961	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs61818772	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818800	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6537740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537741	1.00[JPT][hapmap]
rs6537742	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs6537744	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6537745	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6537746	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6537747	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6658555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659677	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6661642	0.88[EUR][1000 genomes]
rs6663922	0.85[EUR][1000 genomes]
rs6668533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6671645	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6672761	0.88[EUR][1000 genomes]
rs6673930	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6674053	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6674068	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6681371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682678	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6689672	0.84[AFR][1000 genomes]
rs6690169	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6691025	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6691917	0.93[EUR][1000 genomes]
rs6693880	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6696991	0.85[EUR][1000 genomes]
rs6698030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701351	0.93[EUR][1000 genomes]
rs7516421	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7519368	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522110	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7527076	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7535636	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7537789	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7540251	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7542820	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7546203	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7549547	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7551933	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9429694	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9662162	0.80[EUR][1000 genomes]
rs999923	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7415988	ST7L	cis	Nerve Tibial	GTEx
rs7415988	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs7415988	ST7L	cis	lung	GTEx

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	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
3	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
4	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
7	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
9	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:113148200-113159800	Strong transcription	Fetal Intestine Small	intestine
15	chr1:113148800-113160800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:113149200-113159800	Weak transcription	HepG2	liver
17	chr1:113149200-113160000	Weak transcription	Stomach Mucosa	stomach
18	chr1:113149400-113160000	Weak transcription	Pancreas	Pancrea
19	chr1:113150200-113160000	Weak transcription	Right Ventricle	heart
20	chr1:113150200-113160800	Weak transcription	Aorta	Aorta
21	chr1:113151800-113160000	Weak transcription	Colonic Mucosa	Colon
22	chr1:113153400-113160000	Weak transcription	Brain Substantia Nigra	brain
23	chr1:113153400-113160200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:113153400-113160600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:113153600-113159800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:113153600-113159800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:113153600-113159800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:113153600-113160000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:113153600-113160000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:113153600-113160000	Weak transcription	Psoas Muscle	Psoas
31	chr1:113153600-113160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:113153600-113160600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:113153800-113159800	Weak transcription	GM12878-XiMat	blood
34	chr1:113154200-113160000	Weak transcription	NHLF	lung
35	chr1:113154200-113160400	Weak transcription	A549	lung
36	chr1:113155000-113161000	Weak transcription	Esophagus	oesophagus
37	chr1:113155200-113159800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:113155800-113159800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:113155800-113160000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:113155800-113160000	Weak transcription	Brain Anterior Caudate	brain
41	chr1:113156000-113160200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:113156000-113160400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:113156200-113159800	Weak transcription	Primary B cells from cord blood	blood
44	chr1:113156200-113159800	Weak transcription	HMEC	breast
45	chr1:113156200-113160000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:113156600-113159800	Weak transcription	NHDF-Ad	bronchial
47	chr1:113156600-113160000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:113156600-113160200	Weak transcription	NH-A	brain
49	chr1:113156800-113159800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:113156800-113159800	Weak transcription	Monocytes-CD14+_RO01746	blood

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