Variant report

Variant	rs7928842
Chromosome Location	chr11:47566352-47566353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47556325..47561893-chr11:47562676..47568878,7	K562	blood:
2	chr11:47565515..47568693-chr11:47572907..47576173,5	K562	blood:
3	chr11:47557985..47562133-chr11:47565496..47569267,5	K562	blood:
4	chr11:47564735..47568693-chr11:47572355..47576179,6	K562	blood:
5	chr11:47559176..47561794-chr11:47565770..47569453,3	MCF-7	breast:
6	chr11:47565208..47567772-chr11:47587108..47588615,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110536	Chromatin interaction
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1057233	0.95[CHB][hapmap]
rs1064608	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10769258	0.90[CHB][hapmap]
rs10769262	0.95[CHB][hapmap]
rs10838698	0.90[CHB][hapmap]
rs10838699	0.91[CHB][hapmap]
rs10838708	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10838724	0.84[ASN][1000 genomes]
rs10838738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10838747	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10838748	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10838757	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11039212	0.95[CHB][hapmap]
rs11039255	0.81[ASN][1000 genomes]
rs11039307	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11604680	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11605672	0.95[CHB][hapmap]
rs12419692	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12787112	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12794570	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12798028	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12798346	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1317149	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs17788930	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2030166	0.84[ASN][1000 genomes]
rs2053979	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2071304	0.95[CHB][hapmap]
rs2293577	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2293578	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2868459	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34958982	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3781625	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3781626	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3781627	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3817334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3817335	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752845	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4752856	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752857	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752990	0.95[CHB][hapmap]
rs4752993	0.95[CHB][hapmap]
rs4752994	0.95[CHB][hapmap]
rs4752999	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4992357	0.95[CHB][hapmap]
rs56400411	0.86[ASN][1000 genomes]
rs6485753	0.95[CHB][hapmap]
rs66749409	0.87[ASN][1000 genomes]
rs7124681	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs755553	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs755554	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7937331	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7940536	0.95[CHB][hapmap]
rs7945473	0.81[ASN][1000 genomes]
rs896816	0.95[CHB][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	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv314	chr11:47561564-47606256	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7928842	C1QTNF4	cis	multi-tissue	Pritchard
rs7928842	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs7928842	SPI1	cis	multi-tissue	Pritchard
rs7928842	Hs.6637	cis	multi-tissue	Pritchard
rs7928842	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs7928842		cis	Lymphoblastoid	GTEx
rs7928842	C1QTNF4	cis	Muscle Skeletal	GTEx
rs7928842	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7928842	SPI1	cis	Lymphoblastoid	GTEx
rs7928842	MTCH2	cis	cerebellar cortex	BrainEAC

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47546000-47572400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:47546400-47573400	Weak transcription	Colonic Mucosa	Colon
3	chr11:47546400-47573600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47553000-47573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47554400-47572400	Weak transcription	Aorta	Aorta
6	chr11:47554800-47571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:47554800-47572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:47557800-47567000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:47558400-47572600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr11:47559000-47567000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:47559000-47571800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:47559600-47572600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr11:47560400-47567400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr11:47560800-47566600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr11:47561000-47567000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:47561400-47568000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:47561600-47573200	Weak transcription	Placenta	Placenta
18	chr11:47561800-47566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:47562000-47568000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:47562000-47570600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:47562000-47571800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:47562000-47572600	Weak transcription	Brain Substantia Nigra	brain
23	chr11:47562200-47567800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:47562200-47569000	Weak transcription	Pancreas	Pancrea
25	chr11:47562200-47571200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:47562200-47572000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:47562200-47572600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:47562200-47572800	Weak transcription	Fetal Kidney	kidney
29	chr11:47562400-47569200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:47562400-47572200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:47562600-47566400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr11:47562600-47568000	Weak transcription	Small Intestine	intestine
33	chr11:47562600-47569200	Weak transcription	A549	lung
34	chr11:47562600-47569400	Weak transcription	Primary B cells from cord blood	blood
35	chr11:47562600-47570600	Weak transcription	Fetal Brain Female	brain
36	chr11:47562600-47570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:47562600-47571600	Weak transcription	Right Atrium	heart
38	chr11:47562600-47571800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:47562600-47572400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:47562600-47572400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr11:47562600-47572400	Weak transcription	Right Ventricle	heart
42	chr11:47562600-47573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:47562800-47566400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:47562800-47567200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr11:47562800-47568200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr11:47562800-47568200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr11:47562800-47569200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:47562800-47569200	Weak transcription	Osteobl	bone
49	chr11:47562800-47569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:47562800-47570600	Weak transcription	Dnd41	blood

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