Variant report

Variant	rs31304
Chromosome Location	chr5:52942083-52942084
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1844696	1.00[YRI][hapmap]
rs185603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs198941	1.00[YRI][hapmap]
rs2406913	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs269415	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73754279	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881348	chr5:52885100-52942083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs31304	CSF3	trans	brain	seeQTL
rs31304	CXCL11	trans	brain	seeQTL
rs31304	CXCL2	trans	brain	seeQTL
rs31304	CXCL10	trans	brain	seeQTL
rs31304	IL8	trans	brain	seeQTL
rs31304	CXCL1	trans	brain	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52903000-52943800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:52904400-52966600	Weak transcription	Osteobl	bone
3	chr5:52919200-52944000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:52921600-52963400	Weak transcription	A549	lung
6	chr5:52925600-52961200	Weak transcription	Esophagus	oesophagus
7	chr5:52925800-52952000	Weak transcription	Colonic Mucosa	Colon
8	chr5:52926000-52943800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:52926600-52948800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:52926800-52963600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:52927400-52945000	Weak transcription	Fetal Brain Female	brain
12	chr5:52927400-52961000	Weak transcription	Placenta	Placenta
13	chr5:52927600-52942400	Weak transcription	Fetal Thymus	thymus
14	chr5:52927800-52948600	Weak transcription	Pancreas	Pancrea
15	chr5:52927800-52961200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:52927800-52961200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:52927800-52961200	Weak transcription	Thymus	Thymus
18	chr5:52928000-52945000	Weak transcription	Fetal Intestine Small	intestine
19	chr5:52928000-52946000	Weak transcription	Gastric	stomach
20	chr5:52928000-52962200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:52928200-52944000	Weak transcription	GM12878-XiMat	blood
22	chr5:52928600-52944400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:52929000-52981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:52929200-52943200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:52929200-52947600	Weak transcription	Right Ventricle	heart
26	chr5:52929400-52944400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:52929400-52964600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:52931000-52944600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:52933200-52943000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:52933200-52951600	Weak transcription	Aorta	Aorta
31	chr5:52935200-52978000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:52936600-52943200	Weak transcription	Fetal Intestine Large	intestine
33	chr5:52936600-52944000	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:52936600-52948400	Weak transcription	Lung	lung
35	chr5:52936800-52943000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:52936800-52943000	Weak transcription	Left Ventricle	heart
37	chr5:52936800-52943200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:52936800-52943400	Weak transcription	Primary T cells from cord blood	blood
39	chr5:52937200-52942200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:52937200-52942200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr5:52937200-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:52937200-52944400	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:52937200-52963600	Weak transcription	NHLF	lung
44	chr5:52937400-52942400	Enhancers	Fetal Heart	heart
45	chr5:52938200-52945200	Weak transcription	Adipose Nuclei	Adipose
46	chr5:52938200-52954800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:52938200-52970200	Weak transcription	NH-A	brain
48	chr5:52938400-52943000	Weak transcription	Ovary	ovary
49	chr5:52938400-52943200	Weak transcription	HMEC	breast
50	chr5:52938400-52944000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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