Variant report

Variant	rs61669219
Chromosome Location	chr2:113303411-113303412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113238711..113240808-chr2:113302354..113303950,2	K562	blood:
2	chr2:113302234..113303949-chr2:113316673..113319287,3	MCF-7	breast:
3	chr2:113303031..113306151-chr2:113306991..113309484,3	K562	blood:
4	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10169290	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10169344	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10183849	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10200067	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10205187	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13395691	0.90[ASN][1000 genomes]
rs13395779	0.90[ASN][1000 genomes]
rs13412193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13413001	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424021	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1583616	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2241804	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3961914	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59033131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60489148	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60518507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158580	0.91[ASN][1000 genomes]
rs62158582	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158584	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158585	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158586	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158591	0.95[ASN][1000 genomes]
rs62158643	0.91[ASN][1000 genomes]
rs62158644	0.90[ASN][1000 genomes]
rs7565714	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7565827	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9308671	0.85[ASN][1000 genomes]
rs9308672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808491	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3433993	chr2:113303174-113303412	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs61669219	POLR1B	cis	Nerve Tibial	GTEx
rs61669219	POLR1B	cis	Artery Tibial	GTEx
rs61669219	POLR1B	cis	Thyroid	GTEx
rs61669219	POLR1B	cis	Whole Blood	GTEx
rs61669219	POLR1B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113298600-113303600	Active TSS	GM12878-XiMat	blood
2	chr2:113301000-113304600	Weak transcription	Aorta	Aorta
3	chr2:113301200-113303800	Weak transcription	Brain Substantia Nigra	brain
4	chr2:113301200-113304400	Weak transcription	Colonic Mucosa	Colon
5	chr2:113301200-113304600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:113301200-113304600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:113301200-113304600	Weak transcription	Fetal Stomach	stomach
8	chr2:113301200-113304600	Weak transcription	Right Ventricle	heart
9	chr2:113301200-113305000	Weak transcription	NH-A	brain
10	chr2:113301200-113307200	Weak transcription	HSMMtube	muscle
11	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
12	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:113301400-113303600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:113301400-113303600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:113301400-113304400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:113301400-113304600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:113301400-113304600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:113301400-113304600	Weak transcription	Thymus	Thymus
19	chr2:113301400-113304800	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:113301400-113304800	Weak transcription	Fetal Kidney	kidney
21	chr2:113301400-113308800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:113301400-113308800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:113301400-113310000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:113301400-113326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:113301600-113303600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:113301600-113303600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:113301600-113303600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:113301600-113303600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:113301600-113303600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:113301600-113303600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:113301600-113303600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:113301600-113303600	Weak transcription	Liver	Liver
33	chr2:113301600-113303600	Weak transcription	Brain Germinal Matrix	brain
34	chr2:113301600-113303600	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:113301600-113303600	Weak transcription	Esophagus	oesophagus
36	chr2:113301600-113303600	Weak transcription	Fetal Brain Female	brain
37	chr2:113301600-113303600	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:113301600-113303600	Weak transcription	HUVEC	blood vessel
39	chr2:113301600-113303600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:113301600-113303800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:113301600-113303800	Weak transcription	Fetal Intestine Small	intestine
42	chr2:113301600-113303800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:113301600-113304000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:113301600-113304400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:113301600-113304400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:113301600-113304400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:113301600-113304400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:113301600-113304400	Weak transcription	Brain Angular Gyrus	brain
49	chr2:113301600-113304400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:113301600-113304400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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