Variant report

Variant	rs7699978
Chromosome Location	chr4:86936056-86936057
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr4:86935841-86936063	GM12878	blood:	n/a	chr4:86936006-86936017
2	JUND	chr4:86935914-86936105	K562	blood:	n/a	chr4:86935979-86935988
3	NFIC	chr4:86935699-86936183	GM12878	blood:	n/a	n/a
4	EP300	chr4:86935928-86936128	GM12878	blood:	n/a	chr4:86935964-86935973
5	ATF2	chr4:86935786-86936087	GM12878	blood:	n/a	n/a
6	FOXM1	chr4:86935745-86936058	GM12878	blood:	n/a	n/a
7	MAZ	chr4:86935884-86936071	GM12878	blood:	n/a	chr4:86935995-86936004
8	MAX	chr4:86935875-86936073	GM12878	blood:	n/a	chr4:86935995-86936004
9	EBF1	chr4:86935827-86936090	GM12878	blood:	n/a	chr4:86936006-86936017
10	EBF1	chr4:86935701-86936212	GM12878	blood:	n/a	chr4:86936006-86936017
11	RUNX3	chr4:86935693-86936272	GM12878	blood:	n/a	n/a
12	TCF7L2	chr4:86935778-86936124	HEK293	kidney:	n/a	n/a
13	CREB1	chr4:86935828-86936133	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr4:86935828-86936066	H1-hESC	embryonic stem cell:	n/a	chr4:86935979-86935988
15	ATF2	chr4:86935693-86936185	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:86935739-86936224	H1-neurons	neurons:	n/a	n/a
17	EP300	chr4:86935818-86936057	GM12878	blood:	n/a	chr4:86935964-86935973
18	CREB1	chr4:86935863-86936165	GM12878	blood:	n/a	n/a
19	ATF1	chr4:86935821-86936112	K562	blood:	n/a	n/a
20	BCL3	chr4:86935804-86936076	GM12878	blood:	n/a	n/a
21	RUNX3	chr4:86935785-86936153	GM12878	blood:	n/a	n/a
22	CREB1	chr4:86935787-86936118	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr4:86935772-86936136	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000261496	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10001480	0.81[JPT][hapmap]
rs10212744	0.87[JPT][hapmap]
rs12647176	0.81[JPT][hapmap]
rs12647506	0.81[JPT][hapmap]
rs17011286	0.80[ASN][1000 genomes]
rs17011297	0.95[ASN][1000 genomes]
rs2282598	0.87[CHD][hapmap]
rs2575675	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2589506	0.87[CHD][hapmap]
rs2589523	0.95[ASN][1000 genomes]
rs28514916	1.00[ASN][1000 genomes]
rs3775167	0.87[CHD][hapmap]
rs3775182	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4235078	0.82[JPT][hapmap]
rs4334746	0.82[JPT][hapmap]
rs4352468	0.82[JPT][hapmap]
rs4403040	0.82[JPT][hapmap]
rs4407492	0.82[JPT][hapmap]
rs4546235	0.82[JPT][hapmap]
rs4560400	0.81[JPT][hapmap]
rs4693136	0.81[JPT][hapmap]
rs4693757	0.81[JPT][hapmap]
rs6854208	0.81[JPT][hapmap]
rs958	0.87[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7699978	NKX6-1	cis	cerebellum	SCAN
rs7699978	PTPN13	cis	cerebellum	SCAN
rs7699978	AGPAT9	cis	parietal	SCAN
rs7699978	CDS1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86916800-86985400	Weak transcription	Ovary	ovary
2	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
3	chr4:86917400-86940400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:86919400-86941200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:86925400-86937200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:86925600-86937400	Weak transcription	Fetal Kidney	kidney
7	chr4:86928400-86937800	Weak transcription	Fetal Stomach	stomach
8	chr4:86928600-86953400	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:86931600-86937600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:86931800-86937600	Enhancers	Osteobl	bone
11	chr4:86932400-86937600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:86932600-86936400	Weak transcription	HUVEC	blood vessel
13	chr4:86932600-86937800	Weak transcription	Brain Angular Gyrus	brain
14	chr4:86932800-86953800	Weak transcription	Fetal Lung	lung
15	chr4:86933000-86937600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:86933400-86940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:86934200-86942200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:86934200-86953400	Weak transcription	Aorta	Aorta
19	chr4:86934400-86937400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:86934400-86937800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr4:86935000-86936200	Enhancers	Fetal Heart	heart
22	chr4:86935000-86936800	Enhancers	NHDF-Ad	bronchial
23	chr4:86935000-86937400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:86935000-86937600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:86935000-86937600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:86935200-86936600	Enhancers	Right Atrium	heart
27	chr4:86935200-86937400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:86935200-86942200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:86935200-86949200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:86935400-86936400	Weak transcription	NH-A	brain
31	chr4:86935400-86936800	Enhancers	Dnd41	blood
32	chr4:86935400-86937400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:86935400-86937600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:86935400-86938400	Weak transcription	Brain Substantia Nigra	brain
35	chr4:86935600-86936400	Weak transcription	HSMMtube	muscle
36	chr4:86935600-86936600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:86935600-86936600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:86935600-86936800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr4:86935600-86936800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr4:86935600-86936800	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:86935600-86936800	Enhancers	GM12878-XiMat	blood
42	chr4:86935600-86937000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:86935600-86938400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:86935800-86936600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:86935800-86936600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:86935800-86936600	Enhancers	Spleen	Spleen
47	chr4:86935800-86937400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr4:86935800-86937600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:86936000-86936400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr4:86936000-86936400	Weak transcription	NHLF	lung

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