Variant report

Variant	rs11944608
Chromosome Location	chr4:77038643-77038644
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	chr4:77036401..77038944-chr4:77066954..77070829,4	K562	blood:
2	chr4:77037122..77039449-chr4:77042114..77044067,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10008834	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10014749	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10015467	0.94[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015842	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10028141	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097230	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097262	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12331871	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13115827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141895	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13152491	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1348204	0.81[ASN][1000 genomes]
rs17001385	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17001573	0.81[CHB][hapmap]
rs2197104	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28600676	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28611472	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28628345	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28635901	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28649343	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28726273	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28857291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28894799	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34019987	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34023726	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34067866	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34072573	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816248	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4241585	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4241586	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4263427	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339237	0.94[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4515186	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4552491	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532189	0.88[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs9307076	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9307078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers 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 miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11944608	CXCL10	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77031600-77039200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:77032200-77049200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:77032800-77039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:77033000-77044800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:77033000-77046800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr4:77033000-77046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:77033000-77052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:77033200-77038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:77033200-77044400	Weak transcription	Spleen	Spleen
12	chr4:77033200-77045200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:77033200-77045600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr4:77033200-77046200	Strong transcription	Liver	Liver
15	chr4:77033200-77046600	Strong transcription	Fetal Lung	lung
16	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
19	chr4:77033400-77039400	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:77033400-77039800	Strong transcription	HSMM	muscle
21	chr4:77033400-77040600	Weak transcription	Lung	lung
22	chr4:77033400-77041000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:77033400-77041000	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:77033400-77041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:77033400-77042200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:77033400-77043400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:77033400-77045600	Strong transcription	Adipose Nuclei	Adipose
28	chr4:77033400-77046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:77033400-77046000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:77033400-77046200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:77033400-77046400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:77033400-77046600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:77033400-77047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:77033400-77048200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:77033400-77052000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:77033400-77052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:77033600-77047600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:77034000-77039400	Strong transcription	Brain Anterior Caudate	brain
44	chr4:77034000-77045600	Strong transcription	Fetal Intestine Large	intestine
45	chr4:77034000-77046200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:77034000-77054000	Strong transcription	Dnd41	blood
47	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:77034200-77039400	Strong transcription	HUVEC	blood vessel
49	chr4:77034200-77039600	Strong transcription	Fetal Kidney	kidney
50	chr4:77034200-77040800	Strong transcription	Osteobl	bone

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