Variant report

Variant	rs6841880
Chromosome Location	chr4:15813723-15813724
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr4:15813231-15813826	ECC-1	luminal epithelium:	n/a	n/a
2	FOXM1	chr4:15813086-15813770	ECC-1	luminal epithelium:	n/a	n/a
3	FOXM1	chr4:15813089-15813984	ECC-1	luminal epithelium:	n/a	n/a
4	SRF	chr4:15813135-15813888	ECC-1	luminal epithelium:	n/a	n/a
5	SRF	chr4:15813243-15813724	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr4:15813714-15813877	HepG2	liver:	n/a	n/a
7	CEBPB	chr4:15813692-15813943	K562	blood:	n/a	n/a
8	CEBPB	chr4:15813625-15813896	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr4:15813233-15813777	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr4:15813091-15813770	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr4:15813163-15813782	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr4:15813040-15813971	ECC-1	luminal epithelium:	n/a	n/a
13	CEBPB	chr4:15813678-15813919	ECC-1	luminal epithelium:	n/a	n/a
14	TEAD4	chr4:15813241-15813825	ECC-1	luminal epithelium:	n/a	n/a
15	TEAD4	chr4:15813196-15813758	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr4:15813462-15813773	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFIC	chr4:15813198-15813754	ECC-1	luminal epithelium:	n/a	n/a

No data

Variant related genes	Relation type
CD38	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10805347	0.82[JPT][hapmap]
rs16892407	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3756241	0.88[ASN][1000 genomes]
rs3775954	0.89[ASN][1000 genomes]
rs3796863	0.87[ASW][hapmap];0.87[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4516711	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4698420	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6449190	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6831585	0.90[CHD][hapmap]
rs6836946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs6839601	0.86[EUR][1000 genomes]
rs7670690	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv10460	chr4:15757611-15818206	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1013204	chr4:15762970-15836237	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1010597	chr4:15776181-15836237	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	3 gene(s)	inside rSNPs	diseases
5	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6841880	C1QTNF7	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15808400-15819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:15810800-15821600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:15811200-15818600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:15811400-15817800	Weak transcription	Fetal Thymus	thymus
5	chr4:15811400-15818600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr4:15811400-15818600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:15811400-15818800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:15811400-15819400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:15811400-15819800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:15811400-15820000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr4:15811400-15827000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:15811400-15851200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:15811400-15852200	Weak transcription	Spleen	Spleen
14	chr4:15811600-15818000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:15811600-15818200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:15811600-15821600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:15811800-15818000	Weak transcription	Primary T cells from cord blood	blood
18	chr4:15811800-15818200	Weak transcription	Thymus	Thymus
19	chr4:15811800-15819000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:15811800-15842200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:15812200-15840000	Strong transcription	Dnd41	blood
22	chr4:15813200-15813800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:15813200-15813800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:15813200-15813800	Enhancers	HMEC	breast
25	chr4:15813200-15814000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:15813200-15814000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:15813200-15814000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:15813200-15814000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr4:15813200-15814000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:15813200-15814000	Enhancers	NHEK	skin
31	chr4:15813400-15813800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:15813400-15813800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:15813400-15813800	Enhancers	Psoas Muscle	Psoas
34	chr4:15813400-15814000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr4:15813400-15814000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:15813400-15814000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr4:15813400-15814400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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