Variant report

Variant	rs6949989
Chromosome Location	chr7:120641731-120641732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120590021..120592843-chr7:120639404..120643575,5	K562	blood:
2	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
3	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction
ENSG00000106034	Chromatin interaction
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10245811	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10245939	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257314	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10277935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1080807	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953923	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[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];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1118142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11976117	0.82[CHB][hapmap]
rs12706305	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706306	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17535702	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058501	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074577	0.86[ASW][hapmap];0.83[LWK][hapmap]
rs2244863	0.86[ASW][hapmap];0.82[LWK][hapmap]
rs2721341	0.80[ASW][hapmap]
rs2721354	0.80[ASW][hapmap]
rs2721363	0.86[ASW][hapmap];0.82[LWK][hapmap]
rs41690	0.86[ASW][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs6944789	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6956237	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6958635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6960415	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7782014	0.82[CHB][hapmap]
rs7782552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7802570	0.82[CHB][hapmap]
rs7802665	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030988	chr7:120636796-120672504	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6949989	MET	cis	parietal	SCAN
rs6949989	TSPAN12	cis	Artery Tibial	GTEx
rs6949989	NDUFA5	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120634200-120644000	Weak transcription	Spleen	Spleen
2	chr7:120637000-120642000	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:120637000-120646800	Weak transcription	Placenta	Placenta
4	chr7:120637200-120641800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:120637200-120647000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:120637200-120663600	Weak transcription	Right Ventricle	heart
7	chr7:120637400-120642200	Weak transcription	Fetal Heart	heart
8	chr7:120638200-120643600	Weak transcription	Left Ventricle	heart
9	chr7:120638800-120643800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr7:120639000-120645000	Enhancers	Liver	Liver
11	chr7:120640000-120644800	Enhancers	Fetal Stomach	stomach
12	chr7:120640400-120642000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:120640400-120642000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:120640400-120642200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr7:120640400-120642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:120640400-120642200	Weak transcription	Hela-S3	cervix
17	chr7:120640400-120644800	Genic enhancers	HSMM	muscle
18	chr7:120640600-120644000	Enhancers	NHLF	lung
19	chr7:120640600-120644200	Enhancers	Osteobl	bone
20	chr7:120640600-120644400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:120640800-120641800	Enhancers	Colon Smooth Muscle	Colon
22	chr7:120640800-120641800	Weak transcription	Fetal Kidney	kidney
23	chr7:120640800-120641800	Weak transcription	NH-A	brain
24	chr7:120640800-120642200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:120640800-120642200	Weak transcription	HSMMtube	muscle
26	chr7:120640800-120642600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:120640800-120643200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:120640800-120643200	Weak transcription	Aorta	Aorta
29	chr7:120640800-120643600	Weak transcription	Right Atrium	heart
30	chr7:120640800-120643800	Enhancers	Stomach Smooth Muscle	stomach
31	chr7:120640800-120644000	Enhancers	Adipose Nuclei	Adipose
32	chr7:120640800-120646000	Weak transcription	Brain Anterior Caudate	brain
33	chr7:120641000-120642000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:120641000-120642200	Weak transcription	Fetal Lung	lung
35	chr7:120641000-120643600	Enhancers	NHDF-Ad	bronchial
36	chr7:120641200-120641800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:120641200-120642400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:120641400-120641800	Enhancers	Fetal Muscle Leg	muscle
39	chr7:120641400-120642200	Genic enhancers	K562	blood
40	chr7:120641400-120642400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:120641400-120642600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr7:120641600-120641800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:120641600-120642000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr7:120641600-120642000	Enhancers	Psoas Muscle	Psoas
45	chr7:120641600-120642000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:120641600-120642400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr7:120641600-120643000	Weak transcription	Ovary	ovary

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