Variant report

Variant	rs2157062
Chromosome Location	chr3:46451647-46451648
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	POLR2A	chr3:46450527-46452937	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46447015..46450131-chr3:46450692..46453311,4	K562	blood:

Variant related genes	Relation type
ENSG00000223552	TF binding region
ENSG00000121797	Chromatin interaction
ENSG00000223552	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1140865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11574428	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11574429	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11574434	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11574435	0.83[EUR][1000 genomes]
rs11575821	0.93[EUR][1000 genomes]
rs2157061	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2856758	0.95[EUR][1000 genomes]
rs3092960	0.85[EUR][1000 genomes]
rs3136535	0.90[EUR][1000 genomes]
rs34291293	0.92[EUR][1000 genomes]
rs34445878	0.93[EUR][1000 genomes]
rs34971514	0.92[EUR][1000 genomes]
rs35388950	0.92[EUR][1000 genomes]
rs41490645	0.90[EUR][1000 genomes]
rs4452362	0.81[EUR][1000 genomes]
rs57093591	0.85[EUR][1000 genomes]
rs6441977	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs6762266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6770674	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6782522	0.98[EUR][1000 genomes]
rs6787972	0.96[EUR][1000 genomes]
rs6791599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6791789	0.97[EUR][1000 genomes]
rs6798291	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6808835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs762790	0.86[EUR][1000 genomes]
rs7652037	0.93[EUR][1000 genomes]
rs916093	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs916094	0.86[AMR][1000 genomes];0.97[EUR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2157062	CCR5	trans	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46438800-46459800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46448200-46452000	Enhancers	Dnd41	blood
3	chr3:46448600-46460000	Weak transcription	Gastric	stomach
4	chr3:46449200-46451800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:46449400-46453000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:46449600-46452000	Enhancers	K562	blood
7	chr3:46449600-46453800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:46449600-46454000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:46449600-46457600	Weak transcription	Primary B cells from cord blood	blood
10	chr3:46449800-46451800	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:46449800-46452000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:46449800-46453800	Weak transcription	Small Intestine	intestine
13	chr3:46450000-46457600	Weak transcription	Stomach Mucosa	stomach
14	chr3:46450000-46457800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:46450200-46451800	Weak transcription	Right Atrium	heart
16	chr3:46450200-46451800	Weak transcription	HSMMtube	muscle
17	chr3:46450200-46452200	Weak transcription	Placenta	Placenta
18	chr3:46450200-46452400	Weak transcription	NHLF	lung
19	chr3:46450200-46452800	Weak transcription	Colonic Mucosa	Colon
20	chr3:46450200-46454200	Weak transcription	Fetal Lung	lung
21	chr3:46450200-46456800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:46450200-46457400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:46450200-46457600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:46450400-46452200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:46450400-46452600	Enhancers	Thymus	Thymus
26	chr3:46450400-46454200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:46450600-46451800	Weak transcription	Osteobl	bone
28	chr3:46450600-46454000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:46450600-46454000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:46450600-46457000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:46450800-46451800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:46450800-46452200	Enhancers	Primary T cells from cord blood	blood
33	chr3:46450800-46453600	Weak transcription	HUVEC	blood vessel
34	chr3:46450800-46454000	Weak transcription	Psoas Muscle	Psoas
35	chr3:46451000-46451800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:46451000-46451800	Strong transcription	Fetal Intestine Small	intestine
37	chr3:46451000-46452000	Genic enhancers	Lung	lung
38	chr3:46451000-46452400	Enhancers	Fetal Thymus	thymus
39	chr3:46451000-46457600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:46451200-46451800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:46451200-46452600	Enhancers	Adipose Nuclei	Adipose
42	chr3:46451400-46451800	Enhancers	Primary T cells fromperipheralblood	blood
43	chr3:46451400-46451800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:46451400-46452200	Enhancers	Brain Hippocampus Middle	brain
45	chr3:46451600-46451800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:46451600-46451800	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:46451600-46451800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:46451600-46452000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:46451600-46452000	Enhancers	Brain Anterior Caudate	brain
50	chr3:46451600-46452200	Weak transcription	Right Ventricle	heart

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