Variant report

Variant	rs2240859
Chromosome Location	chr3:42787469-42787470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42622067..42623829-chr3:42785959..42788235,2	K562	blood:
2	chr3:42695894..42698650-chr3:42786338..42788734,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KBTBD5-2	chr3:42786435-42788260	ENSG00000173811.6

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10490794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487729	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12491179	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12633707	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635736	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639142	0.87[CHB][hapmap]
rs13070345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339684	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs339731	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34549959	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846063	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3895740	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3907218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912104	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3916334	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60706321	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6807878	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639483	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9830553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9839430	0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2240859	HHATL	cis	cerebellum	SCAN
rs2240859	ZNF35	cis	cerebellum	SCAN
rs2240859	LRRC2	cis	cerebellum	SCAN
rs2240859	HHATL	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42769800-42787600	Weak transcription	Gastric	stomach
2	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
3	chr3:42778200-42788000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:42781000-42788600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr3:42781200-42788600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:42785200-42790200	Enhancers	Brain Anterior Caudate	brain
8	chr3:42785200-42792000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:42785200-42792000	Enhancers	Brain Substantia Nigra	brain
10	chr3:42785400-42787800	Enhancers	Colon Smooth Muscle	Colon
11	chr3:42785400-42787800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:42785400-42788800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:42785400-42790200	Enhancers	Brain Hippocampus Middle	brain
14	chr3:42785400-42792000	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:42785600-42790200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:42785600-42791600	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:42785600-42791800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:42785800-42787800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:42785800-42788000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:42785800-42791800	Enhancers	Fetal Muscle Leg	muscle
21	chr3:42786000-42787800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:42786200-42787600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:42786200-42787600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:42786200-42787600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:42786200-42787600	Weak transcription	Adipose Nuclei	Adipose
26	chr3:42786400-42788400	Enhancers	Fetal Kidney	kidney
27	chr3:42786400-42788600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:42786400-42788800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr3:42786400-42789400	Enhancers	Placenta	Placenta
30	chr3:42786400-42790200	Enhancers	Fetal Stomach	stomach
31	chr3:42786600-42787800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:42786600-42787800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:42786600-42788800	Enhancers	Right Atrium	heart
34	chr3:42786600-42789000	Enhancers	Fetal Lung	lung
35	chr3:42786600-42790000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:42786600-42790400	Enhancers	Brain Angular Gyrus	brain
37	chr3:42786800-42787800	Weak transcription	Pancreas	Pancrea
38	chr3:42786800-42788000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:42786800-42788400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:42786800-42788600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:42787000-42787600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:42787000-42788000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr3:42787000-42788200	Weak transcription	Primary T cells from cord blood	blood
44	chr3:42787000-42788200	Enhancers	Fetal Heart	heart
45	chr3:42787000-42789000	Enhancers	Psoas Muscle	Psoas
46	chr3:42787000-42789200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:42787200-42787800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr3:42787200-42788200	Enhancers	Brain Germinal Matrix	brain
49	chr3:42787200-42789000	Enhancers	Fetal Brain Female	brain
50	chr3:42787200-42789000	Flanking Active TSS	Stomach Smooth Muscle	stomach

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