Variant report

Variant	rs3961775
Chromosome Location	chr2:113302849-113302850
allele	C/T
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	CUX1	chr2:113302810-113302896	GM12878	blood:	n/a	n/a

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	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10153558	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10153801	0.82[ASN][1000 genomes]
rs10864905	0.91[ASN][1000 genomes]
rs11123139	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11123140	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123141	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11675730	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676962	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11677050	0.92[ASN][1000 genomes]
rs11687159	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11689338	0.95[ASN][1000 genomes]
rs12618629	0.87[ASN][1000 genomes]
rs12618882	0.96[ASN][1000 genomes]
rs13015669	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1437673	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1437675	0.98[ASN][1000 genomes]
rs1545133	1.00[ASN][1000 genomes]
rs1595388	0.98[ASN][1000 genomes]
rs2304555	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35832933	0.86[ASN][1000 genomes]
rs3789723	0.96[ASN][1000 genomes]
rs3816140	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816141	0.91[ASN][1000 genomes]
rs3980067	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41278940	0.99[ASN][1000 genomes]
rs41280572	0.91[ASN][1000 genomes]
rs4849072	0.98[ASN][1000 genomes]
rs4849073	0.98[ASN][1000 genomes]
rs4849074	0.98[ASN][1000 genomes]
rs4849075	0.96[ASN][1000 genomes]
rs4849076	0.99[ASN][1000 genomes]
rs56081241	0.91[ASN][1000 genomes]
rs60703755	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs719668	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7568539	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7578724	0.90[ASN][1000 genomes]
rs7607358	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3961775	POLR1B	cis	Skin Sun Exposed Lower leg	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	chr2:113301400-113303200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:113301400-113303600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:113301400-113303600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:113301400-113304400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:113301400-113304600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:113301400-113304600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:113301400-113304600	Weak transcription	Thymus	Thymus
20	chr2:113301400-113304800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:113301400-113304800	Weak transcription	Fetal Kidney	kidney
22	chr2:113301400-113308800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:113301400-113308800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:113301400-113310000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:113301400-113326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:113301600-113303000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:113301600-113303000	Weak transcription	Primary T cells from cord blood	blood
28	chr2:113301600-113303000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr2:113301600-113303200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:113301600-113303400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:113301600-113303400	Weak transcription	Fetal Intestine Large	intestine
32	chr2:113301600-113303600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:113301600-113303600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:113301600-113303600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:113301600-113303600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:113301600-113303600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:113301600-113303600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:113301600-113303600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:113301600-113303600	Weak transcription	Liver	Liver
40	chr2:113301600-113303600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:113301600-113303600	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:113301600-113303600	Weak transcription	Esophagus	oesophagus
43	chr2:113301600-113303600	Weak transcription	Fetal Brain Female	brain
44	chr2:113301600-113303600	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:113301600-113303600	Weak transcription	HUVEC	blood vessel
46	chr2:113301600-113303600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:113301600-113303800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:113301600-113303800	Weak transcription	Fetal Intestine Small	intestine
49	chr2:113301600-113303800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:113301600-113304000	Weak transcription	H1 Cell Line	embryonic stem cell

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