Variant report

Variant	rs11211516
Chromosome Location	chr1:47796110-47796111
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47796071-47796249	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:47795742-47796254	MCF10A-Er-Src	breast:	n/a	chr1:47795968-47795982 chr1:47795965-47795985 chr1:47796019-47796030 chr1:47795971-47795980 chr1:47795969-47795980 chr1:47795970-47795979
3	POLR2A	chr1:47795986-47796328	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:47795757-47796244	MCF10A-Er-Src	breast:	n/a	chr1:47795968-47795982 chr1:47795965-47795985 chr1:47796019-47796030 chr1:47795971-47795980 chr1:47795969-47795980 chr1:47795970-47795979
5	STAT3	chr1:47795740-47796308	MCF10A-Er-Src	breast:	n/a	chr1:47795968-47795982 chr1:47795965-47795985 chr1:47796019-47796030 chr1:47795971-47795980 chr1:47795969-47795980 chr1:47795970-47795979
6	FOS	chr1:47795846-47796143	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:47795825-47796224	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47652463..47655353-chr1:47795985..47798380,2	MCF-7	breast:
2	chr1:47778519..47780256-chr1:47794882..47796645,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMPK1-2	chr1:47795816-47796565	NONHSAT003074

Variant related genes	Relation type
CMPK1	TF binding region
ENSG00000123473	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10157734	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890480	0.80[ASN][1000 genomes]
rs11211489	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211490	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211492	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211495	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211500	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211505	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211512	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211526	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211533	0.80[ASN][1000 genomes]
rs11576796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11577236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577960	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11578360	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11579854	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580114	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11580148	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11583162	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11584518	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587014	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11587107	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11587272	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065137	0.80[ASN][1000 genomes]
rs12080109	0.80[ASN][1000 genomes]
rs12117686	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118205	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12118206	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12123269	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123358	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12129259	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12131978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12132521	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132909	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134888	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135037	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140580	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143808	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12144920	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12145103	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145974	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12184262	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12184269	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12184297	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12406951	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407463	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409300	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12410850	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12718447	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729251	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12735320	0.80[ASN][1000 genomes]
rs12738065	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12749507	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751405	0.80[ASN][1000 genomes]
rs12751618	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756634	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12757893	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12759377	0.86[ASN][1000 genomes]
rs13374382	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13376679	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1572546	0.80[ASN][1000 genomes]
rs17103095	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17103168	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370386	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17378887	0.93[ASN][1000 genomes]
rs2405787	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2622903	0.86[EUR][1000 genomes]
rs2622914	0.87[EUR][1000 genomes]
rs2820986	0.86[EUR][1000 genomes]
rs2897238	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33980430	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34192192	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34979288	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35234940	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35601384	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35856603	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36054263	0.86[ASN][1000 genomes]
rs4375315	0.84[EUR][1000 genomes]
rs4480403	0.80[ASN][1000 genomes]
rs4481897	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926840	0.86[EUR][1000 genomes]
rs56804458	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58891696	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60352530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660651	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6688323	0.89[EUR][1000 genomes]
rs6688804	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6691723	0.80[ASN][1000 genomes]
rs6698471	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698717	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67221389	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67295054	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67905093	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72686209	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7354822	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415976	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525802	0.80[ASN][1000 genomes]
rs7528075	0.86[ASN][1000 genomes]
rs7534328	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548099	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9725517	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11211516	STIL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47780200-47798400	Weak transcription	Spleen	Spleen
2	chr1:47780600-47798000	Weak transcription	HSMMtube	muscle
3	chr1:47780800-47797800	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:47789800-47796200	Weak transcription	K562	blood
5	chr1:47790200-47797400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:47790600-47797000	Weak transcription	Pancreas	Pancrea
7	chr1:47790600-47797800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:47791800-47797600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:47791800-47798200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:47792400-47797600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:47792400-47797800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:47792600-47798000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:47792600-47798400	Weak transcription	Primary T cells from cord blood	blood
14	chr1:47792800-47798600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:47793200-47797600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:47793200-47797800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:47793400-47796600	Weak transcription	Esophagus	oesophagus
18	chr1:47793600-47797400	Weak transcription	Fetal Brain Female	brain
19	chr1:47793600-47798000	Weak transcription	Left Ventricle	heart
20	chr1:47794000-47798200	Weak transcription	Ovary	ovary
21	chr1:47794200-47797800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:47794200-47798000	Weak transcription	Liver	Liver
23	chr1:47794600-47798000	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:47794800-47798000	Weak transcription	Fetal Brain Male	brain
25	chr1:47795200-47796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:47795200-47797800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:47795200-47798200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:47795200-47798200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:47795400-47797400	Weak transcription	Fetal Heart	heart
30	chr1:47795400-47797800	Weak transcription	Fetal Stomach	stomach
31	chr1:47795600-47798600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:47796000-47796200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:47796000-47798200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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