Variant report

Variant	rs6656448
Chromosome Location	chr1:197143278-197143279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10429911	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10732295	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10732296	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10754219	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10801593	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10801594	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1115247	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs1170880	0.85[CEU][hapmap]
rs1170881	0.85[CEU][hapmap]
rs12092294	0.85[CEU][hapmap]
rs12677	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs12731209	0.85[CEU][hapmap]
rs1332662	0.85[CEU][hapmap]
rs1332663	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs1412631	0.85[CEU][hapmap]
rs1412632	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs1412634	0.85[CEU][hapmap]
rs1415217	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1556763	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1571964	0.85[CEU][hapmap]
rs1764629	0.85[EUR][1000 genomes]
rs1764800	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2026429	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs2151134	1.00[CEU][hapmap]
rs4244141	0.98[EUR][1000 genomes]
rs4342879	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4350226	1.00[CEU][hapmap]
rs476390	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4915337	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs4915378	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4915379	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5029273	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs510135	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs518149	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs568757	0.82[EUR][1000 genomes]
rs571106	0.82[EUR][1000 genomes]
rs615647	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs616675	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6428390	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6656858	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs6677082	0.85[CEU][hapmap]
rs6701681	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6703400	0.85[CEU][hapmap]
rs7513826	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7520503	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7523013	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7534353	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs7542397	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs7554802	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7554890	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7554995	0.95[EUR][1000 genomes]
rs877897	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs928439	0.85[CEU][hapmap]
rs928440	0.85[CEU][hapmap]
rs9427660	0.85[CEU][hapmap]
rs9427661	0.85[CEU][hapmap]
rs9427662	0.85[CEU][hapmap]
rs9427942	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116400-197146200	Weak transcription	Gastric	stomach
2	chr1:197116400-197155000	Weak transcription	Fetal Brain Male	brain
3	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:197121600-197154800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:197123800-197147600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:197124600-197155400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:197124800-197144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:197125200-197156000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:197125200-197156400	Weak transcription	Right Ventricle	heart
10	chr1:197125400-197155600	Weak transcription	Fetal Stomach	stomach
11	chr1:197125400-197156200	Weak transcription	Pancreas	Pancrea
12	chr1:197125400-197156400	Weak transcription	Aorta	Aorta
13	chr1:197125400-197156400	Weak transcription	Lung	lung
14	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
15	chr1:197125600-197160000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
17	chr1:197125800-197158400	Weak transcription	Spleen	Spleen
18	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:197127000-197148200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:197128200-197161000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:197128400-197157000	Weak transcription	Colonic Mucosa	Colon
22	chr1:197129000-197155400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:197129200-197149200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:197130200-197145600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:197130200-197148400	Weak transcription	Ovary	ovary
26	chr1:197130200-197149000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:197130200-197156200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:197132400-197148000	Weak transcription	HSMMtube	muscle
29	chr1:197132400-197154800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:197132400-197156400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:197134800-197148000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:197135200-197161800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:197135400-197148200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:197136000-197161600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:197136200-197148000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:197136600-197143400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:197137000-197146600	Strong transcription	HSMM	muscle
38	chr1:197138000-197144200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:197138000-197147400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:197139800-197144400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:197139800-197150600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:197139800-197151000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:197140200-197150600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:197140200-197151800	Weak transcription	Stomach Mucosa	stomach
45	chr1:197140400-197143600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:197140800-197143600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:197140800-197148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:197140800-197151200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:197141000-197146000	Weak transcription	Fetal Lung	lung
50	chr1:197141400-197166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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