Variant report

Variant	rs7679277
Chromosome Location	chr4:74101516-74101517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:74099654..74102966-chr4:74122579..74124991,5	MCF-7	breast:
2	chr4:74099463..74102347-chr4:74103511..74105287,2	MCF-7	breast:
3	chr4:74099672..74104982-chr4:74123482..74126181,5	MCF-7	breast:
4	chr4:74099811..74102120-chr4:74103829..74105781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250220	Chromatin interaction
ENSG00000132466	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10011483	0.80[YRI][hapmap]
rs10019296	0.80[YRI][hapmap]
rs10028486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11933644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651581	0.82[JPT][hapmap]
rs16849102	0.83[ASN][1000 genomes]
rs16849106	0.85[ASN][1000 genomes]
rs16849108	0.85[ASN][1000 genomes]
rs16849146	0.83[ASN][1000 genomes]
rs16849150	0.83[ASN][1000 genomes]
rs16849151	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs16849172	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs16849185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061574	0.85[ASN][1000 genomes]
rs2061575	0.85[ASN][1000 genomes]
rs2061576	0.82[ASN][1000 genomes]
rs2061577	0.85[ASN][1000 genomes]
rs2306057	0.89[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2366716	0.83[ASN][1000 genomes]
rs28373296	0.81[EUR][1000 genomes]
rs28460851	0.81[EUR][1000 genomes]
rs28709646	0.89[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28776801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs3796680	0.81[ASN][1000 genomes]
rs4019514	0.83[ASN][1000 genomes]
rs4631009	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4694589	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56235322	0.84[ASN][1000 genomes]
rs56382488	0.84[ASN][1000 genomes]
rs61149200	0.83[ASN][1000 genomes]
rs61468561	0.83[ASN][1000 genomes]
rs61661011	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6845845	0.94[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[ASN][1000 genomes]
rs6849701	0.87[ASN][1000 genomes]
rs6851670	0.85[ASN][1000 genomes]
rs72663032	0.95[ASN][1000 genomes]
rs72859248	0.83[ASN][1000 genomes]
rs72859249	0.83[ASN][1000 genomes]
rs72861861	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7661799	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7664144	0.80[YRI][hapmap]
rs7670092	0.82[JPT][hapmap]
rs7670286	0.83[ASN][1000 genomes]
rs7674847	0.83[ASN][1000 genomes]
rs7675007	0.84[ASN][1000 genomes]
rs7675027	0.84[ASN][1000 genomes]
rs7676278	0.83[ASN][1000 genomes]
rs7678298	0.82[JPT][hapmap]
rs7687433	0.83[ASN][1000 genomes]
rs7690799	0.83[ASN][1000 genomes]
rs7691344	0.83[ASN][1000 genomes]
rs7692425	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs7692749	0.83[ASN][1000 genomes]
rs7694505	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]

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	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	esv1849323	chr4:73926670-74115116	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1000509	chr4:73968978-74206949	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv879486	chr4:74031423-74114322	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv1793600	chr4:74046221-74116012	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv879489	chr4:74050725-74115116	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	esv3410570	chr4:74055180-74122498	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7679277	C4orf7	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74056000-74123000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:74059600-74123000	Weak transcription	Esophagus	oesophagus
3	chr4:74078200-74123000	Weak transcription	Lung	lung
4	chr4:74087600-74116400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:74087800-74123400	Weak transcription	Gastric	stomach
6	chr4:74088800-74111000	Weak transcription	Colonic Mucosa	Colon
7	chr4:74089000-74121400	Weak transcription	Hela-S3	cervix
8	chr4:74089200-74108800	Weak transcription	Right Ventricle	heart
9	chr4:74089200-74109400	Weak transcription	Fetal Brain Female	brain
10	chr4:74089200-74111000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:74089200-74111600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:74089200-74117600	Weak transcription	NHDF-Ad	bronchial
13	chr4:74089200-74122000	Weak transcription	Aorta	Aorta
14	chr4:74089400-74121800	Weak transcription	NHLF	lung
15	chr4:74089600-74111800	Weak transcription	Fetal Heart	heart
16	chr4:74089800-74112000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:74091000-74102000	Weak transcription	Brain Substantia Nigra	brain
18	chr4:74091000-74111000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:74091200-74103000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:74091200-74107800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:74091200-74110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:74091400-74104000	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:74092600-74101600	Weak transcription	Fetal Intestine Small	intestine
24	chr4:74093200-74116000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:74095400-74104600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:74095800-74105000	Strong transcription	Dnd41	blood
27	chr4:74096200-74102400	Strong transcription	HepG2	liver
28	chr4:74096200-74103600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr4:74096400-74104600	Strong transcription	Fetal Thymus	thymus
30	chr4:74096600-74111000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:74096800-74103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:74097000-74105200	Strong transcription	Primary B cells from cord blood	blood
33	chr4:74097400-74102800	Weak transcription	Brain Germinal Matrix	brain
34	chr4:74097600-74103400	Strong transcription	Primary T cells from cord blood	blood
35	chr4:74097600-74104600	Strong transcription	A549	lung
36	chr4:74097800-74111000	Weak transcription	Psoas Muscle	Psoas
37	chr4:74098000-74102800	Weak transcription	Small Intestine	intestine
38	chr4:74098200-74102200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:74098200-74103200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:74098800-74102200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:74099000-74103400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:74099200-74101600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:74099200-74102200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr4:74099200-74102800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:74099400-74103000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr4:74099400-74103600	ZNF genes & repeats	GM12878-XiMat	blood
47	chr4:74099600-74102400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:74099800-74122400	Weak transcription	Stomach Mucosa	stomach
49	chr4:74100600-74103400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:74100600-74104000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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