Variant report

Variant	rs3800799
Chromosome Location	chr7:40129533-40129534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10156182	0.84[ASN][1000 genomes]
rs10233552	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10234693	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10246466	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1024680	0.82[ASN][1000 genomes]
rs10252631	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10254394	0.84[ASN][1000 genomes]
rs10261984	0.81[EUR][1000 genomes]
rs10272641	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10275761	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10951623	0.98[EUR][1000 genomes]
rs10951624	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10951625	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[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];0.86[ASN][1000 genomes]
rs11972983	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11977756	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[EUR][1000 genomes]
rs11983287	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12334141	0.82[ASN][1000 genomes]
rs12530835	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12531761	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12531774	0.98[EUR][1000 genomes]
rs12532714	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs12533272	0.82[ASN][1000 genomes]
rs12534103	0.95[EUR][1000 genomes]
rs12535281	0.86[EUR][1000 genomes]
rs12536190	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12536349	0.90[EUR][1000 genomes]
rs12536726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12537125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12537320	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12539956	0.95[EUR][1000 genomes]
rs1257698	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12666454	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12669872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12672040	0.95[EUR][1000 genomes]
rs12672136	0.98[EUR][1000 genomes]
rs12672142	0.98[EUR][1000 genomes]
rs13438258	0.86[EUR][1000 genomes]
rs13438262	0.86[EUR][1000 genomes]
rs13438324	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17171637	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17171645	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17171646	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17171658	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs17496429	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17496670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17496733	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17537767	0.98[EUR][1000 genomes]
rs17538125	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2015842	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2052097	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2077124	0.84[ASN][1000 genomes]
rs2109339	0.86[ASN][1000 genomes]
rs2159489	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302341	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[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];0.87[ASN][1000 genomes]
rs2329615	0.86[EUR][1000 genomes]
rs2329693	0.84[ASN][1000 genomes]
rs28627647	0.83[EUR][1000 genomes]
rs28879668	0.86[EUR][1000 genomes]
rs33999222	0.81[ASN][1000 genomes]
rs3735135	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes]
rs3800802	0.84[ASN][1000 genomes]
rs3801238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3847019	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3847020	0.82[ASN][1000 genomes]
rs3911836	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3911889	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4344004	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[EUR][1000 genomes]
rs4720344	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4720347	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4720348	0.84[ASN][1000 genomes]
rs4720349	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4723923	0.98[EUR][1000 genomes]
rs4723925	0.95[EUR][1000 genomes]
rs4723927	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4723928	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60315659	0.98[EUR][1000 genomes]
rs6952597	0.84[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6960111	0.82[ASN][1000 genomes]
rs6961040	0.86[EUR][1000 genomes]
rs6963973	0.86[EUR][1000 genomes]
rs6967332	0.86[EUR][1000 genomes]
rs6970469	0.83[EUR][1000 genomes]
rs731847	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs731848	0.85[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs758696	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs773393	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs773402	0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs773411	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs773424	0.90[CHD][hapmap]
rs7779663	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7797041	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs7799846	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs940272	0.87[EUR][1000 genomes]
rs9639818	0.82[ASN][1000 genomes]
rs9791485	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv464436	chr7:40018693-40133044	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv606706	chr7:40018693-40133044	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv606707	chr7:40021044-40133044	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv606708	chr7:40021044-40157040	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv429748	chr7:40054760-40140660	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv2756801	chr7:40060180-40269583	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	esv2759525	chr7:40060180-40269583	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS 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	17 gene(s)	inside rSNPs	diseases
10	nsv887979	chr7:40067021-40193535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv887980	chr7:40067021-40203356	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS 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	16 gene(s)	inside rSNPs	diseases
12	nsv887981	chr7:40075461-40203356	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv971193	chr7:40075881-40197955	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	esv34547	chr7:40077032-40230965	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv824080	chr7:40077089-40198644	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv464437	chr7:40094641-40197168	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv606709	chr7:40094641-40197168	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv887982	chr7:40098787-40193535	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40072000-40130400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:40080200-40132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:40097200-40132600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:40097200-40132600	Weak transcription	Right Ventricle	heart
5	chr7:40098200-40132400	Weak transcription	Psoas Muscle	Psoas
6	chr7:40099800-40132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:40103000-40131400	Weak transcription	NHLF	lung
8	chr7:40106000-40131400	Weak transcription	HMEC	breast
9	chr7:40116400-40136000	Weak transcription	Fetal Brain Male	brain
10	chr7:40117600-40138000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:40118600-40136600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr7:40119600-40132600	Weak transcription	Small Intestine	intestine
13	chr7:40119800-40135600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:40122400-40135800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:40122800-40137600	Strong transcription	Dnd41	blood
16	chr7:40123400-40131600	Strong transcription	Fetal Muscle Leg	muscle
17	chr7:40124000-40131400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr7:40124000-40134400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:40124000-40135000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:40124000-40137600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr7:40124000-40137800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:40124000-40138400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:40124200-40129600	Strong transcription	Placenta	Placenta
24	chr7:40124400-40136000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:40124400-40136400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:40124400-40137800	Strong transcription	Primary T cells from cord blood	blood
27	chr7:40124800-40134800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:40125000-40130000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:40125000-40133600	Strong transcription	Adipose Nuclei	Adipose
30	chr7:40125000-40137600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:40125200-40135800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:40125800-40135800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:40125800-40136000	Strong transcription	Fetal Thymus	thymus
34	chr7:40125800-40136200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:40125800-40137600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr7:40125800-40137800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr7:40126000-40142400	Weak transcription	Fetal Heart	heart
38	chr7:40126400-40131200	Strong transcription	Fetal Intestine Small	intestine
39	chr7:40126400-40133800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:40126400-40134200	Strong transcription	Fetal Intestine Large	intestine
41	chr7:40126600-40129600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr7:40126600-40130600	Strong transcription	Fetal Stomach	stomach
43	chr7:40126600-40130800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:40126600-40130800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr7:40126600-40131600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:40126600-40132600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:40126600-40135200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:40126600-40136400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:40126600-40137200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:40126800-40129600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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