Variant report

Variant	rs41269993
Chromosome Location	chr1:160968609-160968610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160967045..160969239-chr1:160970582..160972680,3	K562	blood:
2	chr1:160965921..160968886-chr1:161007500..161010236,2	K562	blood:
3	chr1:160965718..160969126-chr1:160976993..160979194,4	K562	blood:
4	chr1:160967186..160969825-chr1:161127897..161129470,2	MCF-7	breast:
5	chr1:160967150..160969611-chr1:160987527..160989808,2	K562	blood:

Variant related genes	Relation type
ENSG00000143258	Chromatin interaction
ENSG00000224985	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000270149	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1044478	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062826	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1062827	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265540	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265542	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11799478	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11799521	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11801586	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11805856	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11807930	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12401336	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405782	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12408778	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565932	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388108	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1806774	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073655	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2073656	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2073658	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2243427	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247459	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247596	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247671	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247790	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251597	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251728	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297219	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297220	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297221	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297222	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2481080	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481081	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481083	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481084	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481085	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2483145	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774274	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2988726	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3119321	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737785	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737787	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs41267947	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267949	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267951	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339888	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55728374	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs61802231	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61803664	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61803665	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61803671	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61803672	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72712854	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812741	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869985	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41269993	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160960000-160970200	Weak transcription	Right Ventricle	heart
2	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
3	chr1:160960600-160968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:160960600-160968800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:160960600-160968800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:160960600-160968800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:160960600-160969000	Weak transcription	Dnd41	blood
8	chr1:160960600-160969600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
10	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
12	chr1:160964400-160968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:160964400-160972600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:160965000-160971800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr1:160965400-160969400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:160965400-160972600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:160965800-160969800	Weak transcription	HSMM	muscle
18	chr1:160966200-160970600	Strong transcription	Fetal Intestine Large	intestine
19	chr1:160966400-160971000	Weak transcription	Psoas Muscle	Psoas
20	chr1:160966600-160971800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:160966600-160971800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:160966800-160971200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:160966800-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:160967000-160969600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:160967000-160971200	Strong transcription	Fetal Thymus	thymus
26	chr1:160967000-160971600	Strong transcription	Esophagus	oesophagus
27	chr1:160967000-160971800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr1:160967000-160971800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:160967000-160972400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:160967400-160969600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:160967400-160970000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:160967400-160971200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:160967400-160972400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:160967600-160968800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:160967600-160969200	Weak transcription	Aorta	Aorta
36	chr1:160967600-160970200	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:160967600-160970400	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:160967600-160970600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:160967600-160971000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:160967600-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr1:160967600-160971000	Strong transcription	GM12878-XiMat	blood
42	chr1:160967600-160971400	Strong transcription	Primary B cells from cord blood	blood
43	chr1:160967600-160971400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:160967600-160971600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:160967600-160971800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:160967600-160971800	Strong transcription	Fetal Stomach	stomach
47	chr1:160967600-160971800	Strong transcription	NHEK	skin
48	chr1:160967600-160972200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:160967600-160972200	Strong transcription	Primary T cells from cord blood	blood
50	chr1:160967600-160972600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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