Variant report

Variant	rs11556146
Chromosome Location	chr4:76569553-76569554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76568880..76572103-chr4:76574675..76578166,4	K562	blood:
2	chr4:76568931..76571295-chr4:76596744..76598717,2	K562	blood:
3	chr4:76438606..76440115-chr4:76567379..76569948,2	K562	blood:

Variant related genes	Relation type
ENSG00000138757	Chromatin interaction
ENSG00000174796	Chromatin interaction
ENSG00000163743	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10856853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097041	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097121	1.00[JPT][hapmap]
rs11723767	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11734358	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11935073	1.00[JPT][hapmap]
rs12498415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12511575	1.00[JPT][hapmap]
rs16996019	0.92[JPT][hapmap]
rs17000786	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17000794	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17000864	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17215400	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17280714	0.85[EUR][1000 genomes]
rs2089253	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs324686	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324690	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs324693	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324703	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324714	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324719	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324723	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324726	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324727	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324733	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324735	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324740	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4262008	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4610362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs60225400	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60945555	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6531816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531934	1.00[JPT][hapmap]
rs6816990	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850797	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856162	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7663617	1.00[JPT][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	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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	24 gene(s)	inside rSNPs	diseases
4	esv1793652	chr4:76521217-76581775	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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 target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11556146	CXCL10	cis	parietal	SCAN
rs11556146	SCARB2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76556200-76590000	Weak transcription	Small Intestine	intestine
2	chr4:76556400-76569800	Weak transcription	Psoas Muscle	Psoas
3	chr4:76556400-76570000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:76556400-76570000	Weak transcription	Fetal Brain Male	brain
5	chr4:76556400-76570200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:76556400-76570600	Weak transcription	Esophagus	oesophagus
7	chr4:76556400-76570600	Weak transcription	Lung	lung
8	chr4:76556400-76570600	Weak transcription	Ovary	ovary
9	chr4:76556400-76570600	Weak transcription	Spleen	Spleen
10	chr4:76556600-76569800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:76556600-76570000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:76556600-76570000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:76556600-76570400	Weak transcription	Fetal Intestine Small	intestine
14	chr4:76556800-76570600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:76562400-76570400	Weak transcription	Right Ventricle	heart
16	chr4:76562800-76569800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:76563000-76570000	Weak transcription	NHLF	lung
18	chr4:76563000-76570600	Weak transcription	Aorta	Aorta
19	chr4:76563800-76569600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:76565000-76584200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:76565600-76588600	Strong transcription	Fetal Thymus	thymus
22	chr4:76565600-76588800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:76566000-76570400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:76566200-76570200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:76566200-76570400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:76566200-76571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:76566200-76596600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:76566400-76570400	Weak transcription	Fetal Stomach	stomach
29	chr4:76566400-76593800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:76566800-76570200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:76566800-76585800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:76567000-76574800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:76567000-76575000	Strong transcription	HMEC	breast
34	chr4:76567000-76588200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:76567000-76588200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:76567200-76579000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:76567200-76585800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:76567200-76586200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:76567400-76574600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr4:76567400-76587400	Strong transcription	Placenta	Placenta
41	chr4:76567400-76588400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:76567400-76588400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:76567400-76596600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:76567600-76569600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:76567600-76569600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:76567600-76587000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr4:76567600-76587200	Strong transcription	Liver	Liver
48	chr4:76567600-76588000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr4:76567600-76588200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:76567600-76588400	Strong transcription	Dnd41	blood

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