Variant report

Variant	rs61818800
Chromosome Location	chr1:113148571-113148572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113148316..113149843-chr1:113151900..113153752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10745332	0.94[ASN][1000 genomes]
rs10857969	0.94[ASN][1000 genomes]
rs11102494	0.82[EUR][1000 genomes]
rs11102508	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102510	0.92[EUR][1000 genomes]
rs11102517	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12048528	0.85[ASN][1000 genomes]
rs12118370	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12119489	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125361	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136781	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12137107	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12138335	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143068	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1238	0.88[ASN][1000 genomes]
rs12402469	0.89[ASN][1000 genomes]
rs12406906	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12739994	0.91[EUR][1000 genomes]
rs12750023	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12758377	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17438324	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273369	0.86[ASN][1000 genomes]
rs2932534	0.95[ASN][1000 genomes]
rs2932535	0.95[ASN][1000 genomes]
rs2932538	0.89[ASN][1000 genomes]
rs2932539	0.89[ASN][1000 genomes]
rs3013441	0.92[ASN][1000 genomes]
rs34531155	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35482634	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36029940	0.82[EUR][1000 genomes]
rs3762335	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790611	0.86[ASN][1000 genomes]
rs3790612	0.91[ASN][1000 genomes]
rs3795820	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4240534	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4838960	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4838961	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4839257	0.88[ASN][1000 genomes]
rs61818772	0.82[EUR][1000 genomes]
rs6537744	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537745	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537746	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537747	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6658555	0.81[EUR][1000 genomes]
rs6659677	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6661642	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663922	0.93[ASN][1000 genomes]
rs6671645	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672761	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6673930	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674053	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674068	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681371	0.82[EUR][1000 genomes]
rs6682678	0.88[ASN][1000 genomes]
rs6690169	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6690292	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6691025	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691917	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693880	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696991	0.92[ASN][1000 genomes]
rs6698030	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6701351	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7415988	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7512984	0.81[ASN][1000 genomes]
rs7516421	0.91[ASN][1000 genomes]
rs7519368	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7522110	0.86[ASN][1000 genomes]
rs7527076	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535636	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7537789	0.91[ASN][1000 genomes]
rs7542820	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546203	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549547	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551933	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552692	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9429694	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662162	0.87[ASN][1000 genomes]
rs999923	0.82[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	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
rs61818800	ST7L	cis	brain	BrainEAC
rs61818800	ST7L	cis	lung	GTEx
rs61818800	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
2	chr1:113109000-113160000	Weak transcription	Gastric	stomach
3	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
5	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
6	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
7	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
11	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
12	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:113133000-113148600	Weak transcription	HSMMtube	muscle
15	chr1:113133000-113152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:113133000-113152400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
18	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:113133200-113148600	Weak transcription	A549	lung
20	chr1:113133200-113149800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:113133200-113150800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:113136200-113156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:113137000-113154200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:113139200-113159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:113139600-113148600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:113140000-113148800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:113140200-113152600	Weak transcription	Primary B cells from cord blood	blood
35	chr1:113140200-113159200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:113140600-113159200	Strong transcription	Fetal Stomach	stomach
38	chr1:113140800-113149000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:113140800-113149000	Weak transcription	Brain Substantia Nigra	brain
40	chr1:113142200-113150000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:113142800-113151000	Weak transcription	K562	blood
42	chr1:113144000-113158600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:113144400-113149000	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:113144600-113150000	Weak transcription	Aorta	Aorta
46	chr1:113145000-113148600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:113145000-113159600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:113145200-113148600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:113145200-113148600	Weak transcription	NHDF-Ad	bronchial
50	chr1:113145200-113148800	Weak transcription	Brain Angular Gyrus	brain

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