Variant report

Variant	rs6973403
Chromosome Location	chr7:39620472-39620473
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:39620146..39620721-chr7:39781543..39782233,2	MCF-7	breast:
2	chr7:39619664..39620687-chr7:39782996..39783915,3	K562	blood:
3	chr7:39620205..39622227-chr7:39661483..39663721,3	K562	blood:
4	chr7:39619675..39620675-chr7:39785462..39786424,9	MCF-7	breast:
5	chr7:39619358..39620673-chr7:39785487..39786442,10	K562	blood:
6	chr7:39617765..39620727-chr7:39709688..39712417,2	K562	blood:
7	chr7:39620191..39622665-chr7:39628141..39629776,2	K562	blood:
8	chr7:39619733..39620697-chr7:39781534..39782496,5	K562	blood:
9	chr7:39619773..39620623-chr7:39785550..39786165,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10232859	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10262131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10486799	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs1051162	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[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];0.97[ASN][1000 genomes]
rs11981810	0.94[ASN][1000 genomes]
rs17171592	0.90[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];0.94[ASN][1000 genomes]
rs17171599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17713701	0.91[ASN][1000 genomes]
rs17714026	0.93[ASN][1000 genomes]
rs17714061	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs17770744	0.93[ASN][1000 genomes]
rs2288744	0.90[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]
rs2876861	0.93[ASN][1000 genomes]
rs2971	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];0.97[ASN][1000 genomes]
rs35586222	0.96[ASN][1000 genomes]
rs59818431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60942815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947660	0.90[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];0.97[ASN][1000 genomes]
rs6978059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73375677	0.97[AFR][1000 genomes]
rs73375682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6973403	C7orf36	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39607000-39623800	Weak transcription	Pancreas	Pancrea
2	chr7:39607000-39631400	Weak transcription	Aorta	Aorta
3	chr7:39607200-39621000	Weak transcription	Right Atrium	heart
4	chr7:39607200-39623200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:39607200-39628800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:39607200-39629000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:39607600-39628600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:39607600-39629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:39607800-39623400	Weak transcription	NHEK	skin
10	chr7:39609800-39622200	Weak transcription	Esophagus	oesophagus
11	chr7:39610400-39620800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:39610800-39628800	Weak transcription	GM12878-XiMat	blood
13	chr7:39612200-39627000	Weak transcription	NHLF	lung
14	chr7:39612400-39626600	Weak transcription	HSMM	muscle
15	chr7:39612400-39628000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:39612600-39628000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:39612600-39629200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:39613400-39628800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:39613800-39621400	Weak transcription	Brain Anterior Caudate	brain
20	chr7:39613800-39627600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:39613800-39628800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:39613800-39629000	Weak transcription	HMEC	breast
23	chr7:39614000-39623000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:39614200-39629200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:39614800-39622800	Weak transcription	Left Ventricle	heart
26	chr7:39614800-39629200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:39616400-39627800	Weak transcription	Adipose Nuclei	Adipose
28	chr7:39616400-39629000	Weak transcription	Osteobl	bone
29	chr7:39616600-39622200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:39617000-39628200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:39617200-39629600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:39617400-39622200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:39617400-39623400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:39617400-39626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:39617400-39629000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:39618400-39620600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr7:39618400-39620800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:39618400-39629000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:39618400-39633000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:39618800-39626400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr7:39619000-39621200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr7:39619000-39622000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:39619000-39622800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:39619000-39628200	Weak transcription	Primary T cells from cord blood	blood
45	chr7:39619000-39629000	Weak transcription	Fetal Thymus	thymus
46	chr7:39619400-39620600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr7:39619400-39622800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr7:39619600-39620600	Enhancers	Fetal Intestine Small	intestine
49	chr7:39619600-39620800	Enhancers	HepG2	liver
50	chr7:39619600-39629000	Weak transcription	Fetal Muscle Leg	muscle

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