Variant report

Variant	rs1978842
Chromosome Location	chr2:86226539-86226540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86225886..86228225-chr2:86420684..86422755,2	K562	blood:
2	chr2:86220130..86224322-chr2:86225400..86228402,3	MCF-7	breast:
3	chr2:86196896..86198796-chr2:86224814..86226828,2	K562	blood:

Variant related genes	Relation type
ENSG00000273080	Chromatin interaction
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10168997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127012	0.93[CEU][hapmap];0.92[GIH][hapmap]
rs11885520	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11895453	0.88[EUR][1000 genomes]
rs11903682	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12124	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1469981	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1469982	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17579744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278532	0.90[JPT][hapmap]
rs3731822	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770086	0.90[JPT][hapmap]
rs3770088	0.81[JPT][hapmap]
rs3770091	0.90[JPT][hapmap]
rs57361751	0.81[ASN][1000 genomes]
rs57405155	0.81[ASN][1000 genomes]
rs58077381	0.88[EUR][1000 genomes]
rs58913632	0.81[ASN][1000 genomes]
rs6707736	0.88[EUR][1000 genomes]
rs6708805	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6741224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72847838	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847843	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72847845	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847853	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7569121	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7599498	1.00[CEU][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9679308	0.82[AMR][1000 genomes];0.85[EUR][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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1978842	POLR1A	cis	parietal	SCAN
rs1978842	POLR1A	cis	multi-tissue	Pritchard
rs1978842	POLR1A	cis	Lymphoblastoid	GTEx
rs1978842	POLR1A	cis	lymphoblastoid	seeQTL
rs1978842	MRPL35	cis	parietal	SCAN
rs1978842	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86219800-86228600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:86219800-86228800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:86219800-86229000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:86219800-86229200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:86220400-86227600	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:86220400-86228800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr2:86220800-86227000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:86220800-86227600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:86220800-86228600	Enhancers	Fetal Muscle Leg	muscle
10	chr2:86220800-86228800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:86220800-86228800	Enhancers	Fetal Thymus	thymus
12	chr2:86221000-86227400	Enhancers	Lung	lung
13	chr2:86221000-86228400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:86221000-86228600	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:86221000-86228600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:86221000-86228600	Enhancers	Spleen	Spleen
17	chr2:86221400-86227600	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:86221400-86228400	Enhancers	Brain Hippocampus Middle	brain
19	chr2:86221400-86228600	Enhancers	Placenta	Placenta
20	chr2:86221600-86228400	Enhancers	Right Atrium	heart
21	chr2:86222600-86226800	Enhancers	Brain Anterior Caudate	brain
22	chr2:86222600-86228400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr2:86222600-86228600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:86222600-86229000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:86222800-86226800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr2:86222800-86228400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:86223200-86226800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:86223200-86227000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:86223200-86227400	Enhancers	Left Ventricle	heart
30	chr2:86223400-86226600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:86223400-86226800	Enhancers	Brain Angular Gyrus	brain
32	chr2:86223400-86227000	Enhancers	Fetal Stomach	stomach
33	chr2:86223400-86227000	Enhancers	Small Intestine	intestine
34	chr2:86223400-86227600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr2:86223400-86228600	Enhancers	Fetal Lung	lung
36	chr2:86223600-86226800	Enhancers	Psoas Muscle	Psoas
37	chr2:86223600-86228400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:86223600-86228600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:86223800-86227000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr2:86223800-86228800	Enhancers	Primary T cells from cord blood	blood
41	chr2:86223800-86228800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:86224000-86227000	Enhancers	Thymus	Thymus
43	chr2:86224000-86227000	Enhancers	A549	lung
44	chr2:86224000-86228600	Enhancers	Fetal Intestine Large	intestine
45	chr2:86224400-86228200	Weak transcription	Esophagus	oesophagus
46	chr2:86224600-86227200	Enhancers	Aorta	Aorta
47	chr2:86224600-86227400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:86224800-86226800	Enhancers	HSMMtube	muscle
49	chr2:86224800-86227000	Enhancers	Fetal Intestine Small	intestine
50	chr2:86225000-86229000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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