Variant report

Variant	rs1583616
Chromosome Location	chr2:113297371-113297372
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113280551..113282537-chr2:113295575..113297853,2	K562	blood:
2	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
3	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:

Variant related genes	Relation type
ENSG00000144130	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10153558	0.88[YRI][hapmap]
rs10169290	0.88[ASN][1000 genomes]
rs10169344	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10183849	0.88[ASN][1000 genomes]
rs10200067	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10205187	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12469608	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs13395691	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13395779	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13412193	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13413001	0.98[ASN][1000 genomes]
rs13424021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241804	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs34179430	0.81[JPT][hapmap]
rs3748026	0.88[CEU][hapmap]
rs3789724	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3961914	0.91[ASN][1000 genomes]
rs59033131	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60489148	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60518507	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61669219	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62158580	0.94[ASN][1000 genomes]
rs62158582	0.97[ASN][1000 genomes]
rs62158584	0.96[ASN][1000 genomes]
rs62158585	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62158586	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62158591	0.94[ASN][1000 genomes]
rs62158643	0.88[ASN][1000 genomes]
rs62158644	0.87[ASN][1000 genomes]
rs7559710	0.81[JPT][hapmap]
rs7565714	0.88[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565827	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7576952	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs9308671	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308672	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9808491	0.86[AMR][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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1583616	POLR1B	cis	Thyroid	GTEx
rs1583616	POLR1B	cis	Nerve Tibial	GTEx
rs1583616	POLR1B	cis	Adipose Subcutaneous	GTEx
rs1583616	POLR1B	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
2	chr2:113270600-113298800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
4	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
5	chr2:113287000-113298800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:113287000-113298800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:113287000-113299000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:113287000-113299000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:113287200-113298800	Weak transcription	Fetal Brain Male	brain
10	chr2:113287200-113298800	Weak transcription	Pancreas	Pancrea
11	chr2:113287200-113299000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:113287400-113298800	Weak transcription	Hela-S3	cervix
13	chr2:113287600-113298600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:113287600-113299000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:113287800-113298800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:113287800-113298800	Weak transcription	Fetal Intestine Large	intestine
17	chr2:113287800-113299000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:113287800-113299000	Weak transcription	Liver	Liver
19	chr2:113287800-113299400	Weak transcription	Spleen	Spleen
20	chr2:113288000-113298600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:113288000-113299000	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:113288200-113298400	Weak transcription	GM12878-XiMat	blood
23	chr2:113288200-113298600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:113288200-113298800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:113288200-113299000	Weak transcription	Right Ventricle	heart
26	chr2:113288200-113299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:113288400-113299000	Weak transcription	Placenta	Placenta
28	chr2:113288800-113298200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:113288800-113299000	Weak transcription	Fetal Lung	lung
30	chr2:113288800-113299200	Weak transcription	Esophagus	oesophagus
31	chr2:113288800-113299200	Weak transcription	Gastric	stomach
32	chr2:113289000-113299000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:113289200-113299000	Weak transcription	Fetal Kidney	kidney
34	chr2:113289400-113298600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:113289400-113299000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:113289600-113298800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:113289600-113299000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:113289800-113298600	Weak transcription	K562	blood
39	chr2:113289800-113298800	Weak transcription	Aorta	Aorta
40	chr2:113289800-113299000	Weak transcription	NHDF-Ad	bronchial
41	chr2:113289800-113299200	Weak transcription	Ovary	ovary
42	chr2:113290000-113298400	Weak transcription	Primary B cells from cord blood	blood
43	chr2:113290000-113298800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:113290000-113298800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:113290000-113298800	Weak transcription	NH-A	brain
46	chr2:113290000-113299000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:113290000-113299000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:113290200-113298600	Weak transcription	Primary T cells from cord blood	blood
49	chr2:113290200-113298800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:113290200-113298800	Weak transcription	Primary monocytes fromperipheralblood	blood

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