Variant report

Variant	rs6678622
Chromosome Location	chr1:78092479-78092480
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	chr1:78081695..78085369-chr1:78091352..78094048,4	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11801808	0.82[YRI][hapmap]
rs12402928	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409142	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12728967	1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12733666	1.00[CHD][hapmap]
rs12741347	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751064	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17381664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909202	1.00[CHD][hapmap]
rs1909203	1.00[CHD][hapmap]
rs1963170	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2647497	1.00[CHD][hapmap]
rs34727511	1.00[CHD][hapmap]
rs4949660	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4949662	1.00[ASW][hapmap];0.92[CEU][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];0.97[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949803	1.00[CHD][hapmap]
rs6684022	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6678622	IFI44	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:78063600-78097600	Weak transcription	Fetal Brain Male	brain
3	chr1:78070600-78098000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:78071000-78098000	Weak transcription	Colonic Mucosa	Colon
5	chr1:78071200-78098000	Weak transcription	Small Intestine	intestine
6	chr1:78071400-78097800	Weak transcription	Aorta	Aorta
7	chr1:78071800-78097800	Weak transcription	Ovary	ovary
8	chr1:78071800-78097800	Weak transcription	Pancreas	Pancrea
9	chr1:78072000-78094600	Weak transcription	Left Ventricle	heart
10	chr1:78072000-78097600	Weak transcription	Gastric	stomach
11	chr1:78072200-78098000	Weak transcription	Spleen	Spleen
12	chr1:78072400-78097800	Weak transcription	Lung	lung
13	chr1:78072600-78097800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:78073200-78097400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:78075000-78096000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:78075000-78097800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:78075200-78098000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:78075400-78097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:78075600-78095800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:78075600-78097600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:78076400-78113000	Weak transcription	Psoas Muscle	Psoas
22	chr1:78077400-78096400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:78077600-78095600	Weak transcription	Adipose Nuclei	Adipose
24	chr1:78080800-78098200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:78083400-78097400	Weak transcription	NHEK	skin
26	chr1:78083600-78095000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:78084200-78097800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:78084200-78097800	Weak transcription	Thymus	Thymus
29	chr1:78084400-78095800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:78084400-78097400	Weak transcription	K562	blood
31	chr1:78085200-78097800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:78085400-78104600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:78086200-78100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:78086400-78097400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:78086400-78100200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:78086400-78104400	Weak transcription	Stomach Mucosa	stomach
37	chr1:78086600-78095000	Weak transcription	A549	lung
38	chr1:78086600-78095400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:78087200-78094600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:78088000-78095000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:78088000-78095000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:78088000-78095000	Weak transcription	Fetal Stomach	stomach
43	chr1:78088000-78095800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:78088800-78097800	Weak transcription	Esophagus	oesophagus
45	chr1:78089000-78097400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:78089400-78097400	Weak transcription	Brain Angular Gyrus	brain
47	chr1:78089400-78097400	Weak transcription	Brain Substantia Nigra	brain
48	chr1:78089400-78097600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:78089400-78097800	Weak transcription	Brain Anterior Caudate	brain
50	chr1:78089400-78098000	Weak transcription	Brain Cingulate Gyrus	brain

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