Variant report

Variant	rs6741224
Chromosome Location	chr2:86245417-86245418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86243376..86246282-chr2:86255772..86258201,2	K562	blood:
2	chr2:86240930..86243180-chr2:86244397..86245985,2	K562	blood:

Variant related genes	Relation type
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10168997	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11127012	0.93[CEU][hapmap]
rs11885520	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11886175	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11895453	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11903682	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12124	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs13390107	0.83[AMR][1000 genomes]
rs1469981	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469982	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17579744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1978842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278532	0.91[JPT][hapmap]
rs311587	0.89[AFR][1000 genomes]
rs3731822	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs3770086	0.91[JPT][hapmap]
rs3770088	0.82[JPT][hapmap]
rs3770091	0.91[JPT][hapmap]
rs57339071	0.83[AMR][1000 genomes]
rs57361751	0.80[ASN][1000 genomes]
rs57405155	0.80[ASN][1000 genomes]
rs58077381	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58913632	0.80[ASN][1000 genomes]
rs6707736	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6708805	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749218	0.83[AMR][1000 genomes]
rs6752561	0.81[AMR][1000 genomes]
rs72847838	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72847843	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72847845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72847853	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7569121	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7599498	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9679308	0.96[AMR][1000 genomes];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6741224	POLR1A	cis	multi-tissue	Pritchard
rs6741224	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86242200-86246200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:86242200-86251200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:86242600-86245800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:86242600-86246800	Enhancers	Fetal Thymus	thymus
5	chr2:86243600-86246400	Enhancers	Thymus	Thymus
6	chr2:86243600-86246600	Enhancers	GM12878-XiMat	blood
7	chr2:86243800-86245600	Enhancers	Lung	lung
8	chr2:86243800-86245800	Enhancers	Adipose Nuclei	Adipose
9	chr2:86243800-86246200	Enhancers	Fetal Muscle Leg	muscle
10	chr2:86243800-86246200	Enhancers	Psoas Muscle	Psoas
11	chr2:86244000-86245600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:86244000-86246000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:86244000-86246400	Enhancers	Pancreas	Pancrea
14	chr2:86244000-86251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:86244200-86246000	Enhancers	Brain Cingulate Gyrus	brain
16	chr2:86244200-86246200	Enhancers	Brain Hippocampus Middle	brain
17	chr2:86244200-86248200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:86244200-86248600	Weak transcription	Right Atrium	heart
19	chr2:86244200-86257000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:86244400-86246200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr2:86244400-86246400	Enhancers	Primary B cells from peripheral blood	blood
22	chr2:86244400-86247800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:86244400-86252400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:86244400-86252600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:86244400-86252800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:86244400-86253000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:86244400-86255000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:86244600-86246000	Enhancers	K562	blood
29	chr2:86244600-86246400	Enhancers	Primary B cells from cord blood	blood
30	chr2:86244600-86248000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:86244600-86251000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:86244600-86251200	Weak transcription	Primary T cells from cord blood	blood
33	chr2:86244600-86251400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:86244600-86251400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:86244600-86251800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:86244600-86252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:86244600-86252600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:86244600-86255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:86244600-86257200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:86244800-86245600	Enhancers	Left Ventricle	heart
41	chr2:86244800-86245600	Enhancers	Right Ventricle	heart
42	chr2:86244800-86245600	Enhancers	Spleen	Spleen
43	chr2:86244800-86245600	Enhancers	HMEC	breast
44	chr2:86244800-86245600	Enhancers	HUVEC	blood vessel
45	chr2:86244800-86246000	Enhancers	Brain Angular Gyrus	brain
46	chr2:86244800-86246000	Enhancers	Brain Anterior Caudate	brain
47	chr2:86244800-86246000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:86244800-86246200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:86244800-86246600	Enhancers	Brain Substantia Nigra	brain
50	chr2:86244800-86253600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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