Variant report

Variant	rs2276441
Chromosome Location	chr11:77702033-77702034
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77699025..77702631-chr11:77704128..77707034,4	K562	blood:
2	chr11:77701991..77703904-chr11:77704276..77705898,2	MCF-7	breast:
3	chr11:77530485..77532728-chr11:77700651..77703314,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149262	Chromatin interaction
ENSG00000087884	Chromatin interaction
ENSG00000048649	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10751278	0.85[EUR][1000 genomes]
rs10793265	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237339	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783546	0.90[CHB][hapmap]
rs1790246	0.85[CHB][hapmap]
rs1790250	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1793343	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs1823508	0.82[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2034499	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2510967	0.82[CHB][hapmap]
rs3018164	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3018412	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs597346	0.87[CEU][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs628198	0.83[EUR][1000 genomes]
rs630274	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs630711	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6592747	0.90[EUR][1000 genomes]
rs6592752	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592753	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592756	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs669869	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672460	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7110670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127510	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7931392	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7938133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7938648	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7941732	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9988883	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276441	INTS4	cis	multi-tissue	Pritchard
rs2276441	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:77664200-77704000	Weak transcription	NHEK	skin
3	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:77667600-77704200	Weak transcription	NHLF	lung
6	chr11:77671200-77704200	Weak transcription	NHDF-Ad	bronchial
7	chr11:77672000-77703800	Weak transcription	Fetal Brain Male	brain
8	chr11:77679000-77704200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:77681000-77704200	Weak transcription	HSMMtube	muscle
10	chr11:77684200-77702400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:77688200-77704800	Weak transcription	Stomach Mucosa	stomach
12	chr11:77688400-77702200	Strong transcription	Dnd41	blood
13	chr11:77688600-77702800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:77688800-77702400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr11:77688800-77702400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:77688800-77703400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:77688800-77703400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:77688800-77703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:77689000-77702600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:77689000-77704800	Weak transcription	Fetal Heart	heart
21	chr11:77689200-77703000	Strong transcription	Primary T cells from cord blood	blood
22	chr11:77689200-77704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:77689600-77703000	Strong transcription	Fetal Thymus	thymus
24	chr11:77690400-77704200	Weak transcription	HMEC	breast
25	chr11:77690600-77703800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:77690600-77704000	Weak transcription	Brain Anterior Caudate	brain
27	chr11:77690600-77704000	Weak transcription	Brain Substantia Nigra	brain
28	chr11:77690600-77704200	Weak transcription	Gastric	stomach
29	chr11:77690600-77704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:77690600-77704400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:77690800-77704200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:77690800-77704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:77690800-77704200	Weak transcription	Small Intestine	intestine
34	chr11:77691400-77704000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:77691400-77704800	Weak transcription	Colonic Mucosa	Colon
36	chr11:77692000-77704000	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:77692600-77704000	Weak transcription	A549	lung
38	chr11:77692600-77704200	Weak transcription	HUVEC	blood vessel
39	chr11:77695400-77702600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:77696000-77702400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr11:77696000-77703000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:77696200-77703400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:77696400-77702400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:77696400-77704400	Weak transcription	Fetal Kidney	kidney
45	chr11:77696600-77702600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:77696800-77702400	Strong transcription	Liver	Liver
47	chr11:77696800-77703200	Strong transcription	Adipose Nuclei	Adipose
48	chr11:77696800-77703400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:77697000-77702600	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:77697000-77703200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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