Variant report

Variant	rs6980244
Chromosome Location	chr7:104636940-104636941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010340	0.81[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs1011468	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10228174	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10247691	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10252714	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10263499	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11978288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1558048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs17640472	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2074753	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs2097942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs2106500	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299298	0.86[EUR][1000 genomes]
rs2299305	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4602821	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4727618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730066	0.90[CHD][hapmap];0.93[ASN][1000 genomes]
rs56016333	0.86[ASN][1000 genomes]
rs6466035	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67665940	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6947388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs6974874	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs6976394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs888086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv437561	chr7:104626690-104647571	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv437995	chr7:104632980-104641241	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1022083	chr7:104634376-104644391	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104625000-104641200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:104625000-104647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:104625200-104643800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:104625400-104643000	Weak transcription	Fetal Brain Female	brain
5	chr7:104625800-104641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:104626200-104641600	Weak transcription	Brain Germinal Matrix	brain
7	chr7:104626400-104639600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:104627000-104641000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:104627200-104638400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:104627400-104643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:104627800-104637600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:104629800-104640200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:104629800-104641200	Weak transcription	Colonic Mucosa	Colon
14	chr7:104630000-104637800	Strong transcription	Dnd41	blood
15	chr7:104630200-104641200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:104630800-104639000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:104630800-104640200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:104630800-104641600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:104630800-104643600	Weak transcription	Fetal Kidney	kidney
20	chr7:104631600-104639000	Strong transcription	K562	blood
21	chr7:104631600-104643600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:104632000-104637600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:104632000-104637800	Strong transcription	GM12878-XiMat	blood
24	chr7:104632000-104641200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:104632200-104640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:104632200-104641200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:104632200-104641200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:104632200-104641200	Weak transcription	Esophagus	oesophagus
29	chr7:104632200-104641200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:104632200-104641200	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:104632200-104641200	Weak transcription	Gastric	stomach
32	chr7:104632200-104641200	Weak transcription	Pancreas	Pancrea
33	chr7:104632200-104641200	Weak transcription	Spleen	Spleen
34	chr7:104632800-104641200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:104632800-104641200	Weak transcription	Fetal Stomach	stomach
36	chr7:104632800-104641400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:104633000-104642600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:104633200-104638200	Strong transcription	Hela-S3	cervix
39	chr7:104633200-104643600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr7:104633400-104638000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:104633400-104639000	Enhancers	Colon Smooth Muscle	Colon
42	chr7:104633400-104641400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr7:104633600-104637200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:104633600-104637200	Strong transcription	Fetal Thymus	thymus
45	chr7:104633600-104637200	Strong transcription	HMEC	breast
46	chr7:104633600-104650400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr7:104634000-104637200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr7:104634000-104637200	Weak transcription	Left Ventricle	heart
49	chr7:104634000-104637200	Weak transcription	Lung	lung
50	chr7:104634000-104647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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