Variant report

Variant	rs9662162
Chromosome Location	chr1:113198091-113198092
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113195577..113199983-chr1:113200406..113202808,3	K562	blood:
2	chr1:113057544..113060149-chr1:113196498..113199134,2	K562	blood:
3	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
4	chr1:113196985..113198858-chr1:113200988..113203460,2	K562	blood:

Variant related genes	Relation type
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10745332	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10857969	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102508	0.84[ASN][1000 genomes]
rs12048528	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12118370	0.83[ASN][1000 genomes]
rs12119489	0.84[ASN][1000 genomes]
rs12125361	0.87[ASN][1000 genomes]
rs12126494	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12137107	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12143068	0.84[ASN][1000 genomes]
rs1238	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12406906	0.84[ASN][1000 genomes]
rs12750023	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12750621	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12758377	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17438324	0.82[ASN][1000 genomes]
rs2932529	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2932534	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932535	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932538	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932539	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3013433	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3013441	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35482634	0.82[ASN][1000 genomes]
rs3762335	0.82[ASN][1000 genomes]
rs3795820	0.81[EUR][1000 genomes]
rs4240534	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4838960	0.83[ASN][1000 genomes]
rs4838961	0.81[AMR][1000 genomes]
rs4839257	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61818800	0.87[ASN][1000 genomes]
rs6537744	0.80[ASN][1000 genomes]
rs6537745	0.87[ASN][1000 genomes]
rs6537746	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6537747	0.83[ASN][1000 genomes]
rs6659677	0.80[ASN][1000 genomes]
rs6663922	0.80[ASN][1000 genomes]
rs6671645	0.84[ASN][1000 genomes]
rs6673930	0.82[ASN][1000 genomes]
rs6674053	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6674068	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6682678	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6690169	0.84[ASN][1000 genomes]
rs6690292	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691025	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6691917	0.84[ASN][1000 genomes]
rs6693880	0.82[ASN][1000 genomes]
rs6701351	0.84[ASN][1000 genomes]
rs7415988	0.80[EUR][1000 genomes]
rs7512984	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7527076	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7535636	0.82[ASN][1000 genomes]
rs7542820	0.84[ASN][1000 genomes]
rs7546203	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9429694	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs999923	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9662162	ST7L	cis	lung	GTEx
rs9662162	ST7L	cis	Nerve Tibial	GTEx
rs9662162	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
2	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
5	chr1:113168800-113199800	Weak transcription	Esophagus	oesophagus
6	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
7	chr1:113175200-113199800	Weak transcription	Psoas Muscle	Psoas
8	chr1:113175200-113200000	Weak transcription	Right Atrium	heart
9	chr1:113176000-113199200	Weak transcription	Fetal Brain Female	brain
10	chr1:113179000-113215600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:113180000-113216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:113180200-113199800	Weak transcription	Spleen	Spleen
13	chr1:113180200-113200800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:113180200-113203000	Weak transcription	Aorta	Aorta
15	chr1:113180800-113200000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:113181200-113201000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:113184200-113215600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:113184600-113214800	Strong transcription	Hela-S3	cervix
19	chr1:113184800-113199800	Weak transcription	Brain Angular Gyrus	brain
20	chr1:113185000-113214800	Strong transcription	Dnd41	blood
21	chr1:113185400-113216200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:113186000-113210800	Strong transcription	GM12878-XiMat	blood
23	chr1:113186000-113214800	Strong transcription	Fetal Thymus	thymus
24	chr1:113186000-113215000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:113186200-113215400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:113187000-113213200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:113187000-113215200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:113187200-113215200	Strong transcription	HSMM	muscle
29	chr1:113187400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:113187800-113201400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:113187800-113202800	Weak transcription	Small Intestine	intestine
32	chr1:113187800-113204000	Weak transcription	Right Ventricle	heart
33	chr1:113187800-113216000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:113188000-113199200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:113188000-113200600	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:113188200-113200800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:113188400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:113188800-113213800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:113189000-113213800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:113189200-113203600	Weak transcription	Gastric	stomach
41	chr1:113189200-113203800	Weak transcription	Pancreas	Pancrea
42	chr1:113189200-113211000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:113189200-113214600	Strong transcription	NHEK	skin
44	chr1:113189200-113214800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:113189200-113215000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:113189400-113214800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:113189800-113199400	Strong transcription	HMEC	breast
48	chr1:113189800-113213800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:113189800-113215200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:113189800-113215400	Strong transcription	Placenta	Placenta

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