Variant report

Variant	rs10857969
Chromosome Location	chr1:113191184-113191185
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113189515..113191899-chr1:113216631..113218383,2	MCF-7	breast:
2	chr1:113178255..113183299-chr1:113188318..113192161,4	K562	blood:
3	chr1:113172398..113173913-chr1:113190499..113193420,2	K562	blood:
4	chr1:113170754..113173551-chr1:113190462..113192444,2	MCF-7	breast:
5	chr1:113185627..113187951-chr1:113190592..113192207,2	K562	blood:
6	chr1:113190577..113193276-chr1:113208144..113210064,2	K562	blood:
7	chr1:113188560..113193477-chr1:113242555..113247444,5	K562	blood:
8	chr1:113180385..113183307-chr1:113188494..113191226,2	MCF-7	breast:

No data

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

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10745332	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102508	0.92[ASN][1000 genomes]
rs11102510	0.82[EUR][1000 genomes]
rs11102517	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12048528	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118370	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12119489	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12125361	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126494	0.90[EUR][1000 genomes]
rs12136781	0.85[ASN][1000 genomes]
rs12137107	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138335	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12143068	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1238	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402469	0.83[ASN][1000 genomes]
rs12406906	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12739994	0.81[EUR][1000 genomes]
rs12750023	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12750621	0.91[EUR][1000 genomes]
rs12758377	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17438324	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2273369	0.81[ASN][1000 genomes]
rs2932529	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2932534	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932535	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932538	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932539	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3013433	0.87[EUR][1000 genomes]
rs3013441	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34531155	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35482634	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3762335	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3790611	0.81[ASN][1000 genomes]
rs3790612	0.85[ASN][1000 genomes]
rs3795820	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4240534	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838960	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838961	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4839257	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61818800	0.94[ASN][1000 genomes]
rs6537744	0.88[ASN][1000 genomes]
rs6537745	0.94[ASN][1000 genomes]
rs6537746	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537747	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6659677	0.83[ASN][1000 genomes]
rs6661642	0.85[ASN][1000 genomes]
rs6663922	0.88[ASN][1000 genomes]
rs6671645	0.92[ASN][1000 genomes]
rs6672761	0.84[ASN][1000 genomes]
rs6673930	0.90[ASN][1000 genomes]
rs6674053	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674068	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6682678	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6690169	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6690292	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691025	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691917	0.92[ASN][1000 genomes]
rs6693880	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6696991	0.86[ASN][1000 genomes]
rs6698030	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6701351	0.92[ASN][1000 genomes]
rs7415988	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7512984	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7516421	0.85[ASN][1000 genomes]
rs7522110	0.81[ASN][1000 genomes]
rs7527076	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535636	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7537789	0.85[ASN][1000 genomes]
rs7542820	0.92[ASN][1000 genomes]
rs7546203	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7549547	0.85[ASN][1000 genomes]
rs7551933	0.85[ASN][1000 genomes]
rs7552692	0.84[ASN][1000 genomes]
rs9429694	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662162	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs999923	0.83[AMR][1000 genomes];0.90[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
rs10857969	ST7L	cis	Nerve Tibial	GTEx
rs10857969	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs10857969	ST7L	cis	lung	GTEx

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	chr1:113172600-113191400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:113175200-113199800	Weak transcription	Psoas Muscle	Psoas
9	chr1:113175200-113200000	Weak transcription	Right Atrium	heart
10	chr1:113176000-113199200	Weak transcription	Fetal Brain Female	brain
11	chr1:113178200-113191400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:113179000-113215600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:113179400-113191400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:113179600-113197400	Weak transcription	Colonic Mucosa	Colon
15	chr1:113179800-113191400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:113180000-113191400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:113180000-113193800	Weak transcription	Stomach Mucosa	stomach
18	chr1:113180000-113216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:113180200-113191600	Weak transcription	NHLF	lung
20	chr1:113180200-113199800	Weak transcription	Spleen	Spleen
21	chr1:113180200-113200800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:113180200-113203000	Weak transcription	Aorta	Aorta
23	chr1:113180400-113193200	Weak transcription	HSMMtube	muscle
24	chr1:113180800-113191400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:113180800-113191600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:113180800-113200000	Weak transcription	Brain Anterior Caudate	brain
27	chr1:113181200-113194000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:113181200-113201000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:113182400-113191800	Weak transcription	A549	lung
30	chr1:113184200-113215600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:113184400-113192000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:113184600-113214800	Strong transcription	Hela-S3	cervix
33	chr1:113184800-113199800	Weak transcription	Brain Angular Gyrus	brain
34	chr1:113185000-113214800	Strong transcription	Dnd41	blood
35	chr1:113185400-113216200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:113186000-113210800	Strong transcription	GM12878-XiMat	blood
37	chr1:113186000-113214800	Strong transcription	Fetal Thymus	thymus
38	chr1:113186000-113215000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:113186200-113215400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:113187000-113213200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:113187000-113215200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:113187200-113215200	Strong transcription	HSMM	muscle
43	chr1:113187400-113215000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:113187800-113191200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:113187800-113191400	Weak transcription	Brain Substantia Nigra	brain
46	chr1:113187800-113192200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:113187800-113195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:113187800-113201400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:113187800-113202800	Weak transcription	Small Intestine	intestine
50	chr1:113187800-113204000	Weak transcription	Right Ventricle	heart

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