Variant report

Variant	rs6431653
Chromosome Location	chr2:234940630-234940631
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	chr2:234939882..234942126-chr2:234943177..234946167,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12615187	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12624062	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395835	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395836	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17864793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17869090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362296	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6758440	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460138	chr2:234933559-234944043	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv584709	chr2:234933559-234944043	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv522778	chr2:234933630-234944043	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv524821	chr2:234933630-234944043	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv470524	chr2:234933630-234944043	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv584710	chr2:234933630-234945670	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv584711	chr2:234934186-234945105	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
11	esv2760543	chr2:234938082-234955890	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
12	nsv1006508	chr2:234938781-234955878	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
13	nsv437316	chr2:234939481-234956344	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
14	nsv1003303	chr2:234940575-234955878	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6431653	UGT1A1	cis	cerebellum	SCAN
rs6431653	PDE6D	cis	parietal	SCAN
rs6431653	NEK3	trans	cerebellum	SCAN
rs6431653	NCL	cis	parietal	SCAN
rs6431653	ASB18	cis	cerebellum	SCAN
rs6431653	SPP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234934600-234940800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:234934800-234942400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:234935800-234940800	Weak transcription	HSMM	muscle
4	chr2:234937800-234942200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:234938000-234942000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:234939000-234942000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:234939000-234942200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr2:234939200-234941600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:234939200-234941800	Enhancers	NHDF-Ad	bronchial
10	chr2:234939400-234941600	Enhancers	Osteobl	bone
11	chr2:234939400-234942200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr2:234939400-234942400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:234939400-234942400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:234939600-234941000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:234939600-234941800	Enhancers	NHEK	skin
16	chr2:234939600-234942000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:234939600-234942200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:234939600-234942200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:234939800-234941800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:234939800-234941800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:234939800-234942200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:234939800-234942200	Enhancers	HMEC	breast
23	chr2:234940000-234940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:234940000-234940800	Weak transcription	A549	lung
25	chr2:234940000-234941800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:234940000-234942000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:234940000-234942200	Enhancers	NH-A	brain
28	chr2:234940400-234941800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr2:234940400-234942200	Enhancers	HUVEC	blood vessel
30	chr2:234940600-234941000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:234940600-234941600	Weak transcription	NHLF	lung

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