Variant report

Variant	rs12190099
Chromosome Location	chr6:119142264-119142265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10456918	0.88[EUR][1000 genomes]
rs11153777	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11153778	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11153780	0.88[EUR][1000 genomes]
rs11153791	0.88[EUR][1000 genomes]
rs12194135	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12194458	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12202077	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204825	0.89[EUR][1000 genomes]
rs12207663	0.88[EUR][1000 genomes]
rs12211553	1.00[ASN][1000 genomes]
rs12213327	0.88[EUR][1000 genomes]
rs17506361	0.89[EUR][1000 genomes]
rs67182660	0.87[EUR][1000 genomes]
rs67456868	1.00[AMR][1000 genomes]
rs6902942	0.88[EUR][1000 genomes]
rs7772912	0.89[EUR][1000 genomes]
rs7775275	0.87[EUR][1000 genomes]
rs9374756	0.87[EUR][1000 genomes]
rs9374760	0.88[EUR][1000 genomes]
rs9374762	0.88[EUR][1000 genomes]
rs9401101	0.90[EUR][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	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS 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	10 gene(s)	inside rSNPs	diseases
2	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers 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
3	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119122000-119147000	Weak transcription	Stomach Mucosa	stomach
2	chr6:119122200-119147000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:119122400-119146800	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:119122600-119144000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:119125600-119143600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:119128600-119151600	Weak transcription	Colonic Mucosa	Colon
7	chr6:119130600-119146400	Weak transcription	Psoas Muscle	Psoas
8	chr6:119130800-119143000	Weak transcription	Fetal Lung	lung
9	chr6:119132200-119143000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:119132200-119143600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:119132200-119145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:119132200-119146400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:119132200-119150600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:119132400-119146800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:119132400-119150800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:119133400-119148000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:119133400-119151800	Weak transcription	Fetal Kidney	kidney
18	chr6:119134000-119150600	Weak transcription	Hela-S3	cervix
19	chr6:119134200-119143600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:119134200-119143600	Weak transcription	HUVEC	blood vessel
21	chr6:119134200-119144000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:119134400-119143600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:119134400-119146600	Weak transcription	Brain Anterior Caudate	brain
24	chr6:119134400-119146800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:119134400-119147000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:119134400-119147000	Weak transcription	Small Intestine	intestine
27	chr6:119135000-119146600	Weak transcription	GM12878-XiMat	blood
28	chr6:119135200-119150600	Weak transcription	NHLF	lung
29	chr6:119135400-119146600	Weak transcription	HMEC	breast
30	chr6:119135400-119146600	Weak transcription	NHEK	skin
31	chr6:119135400-119146600	Weak transcription	Osteobl	bone
32	chr6:119135400-119149000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:119135400-119150200	Weak transcription	Brain Substantia Nigra	brain
34	chr6:119135400-119151000	Weak transcription	NH-A	brain
35	chr6:119135400-119151400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:119135600-119142800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:119135600-119146200	Weak transcription	HSMM	muscle
38	chr6:119135800-119146200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:119135800-119151000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:119136800-119143600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:119137000-119143400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:119137000-119144000	Weak transcription	Brain Germinal Matrix	brain
43	chr6:119137200-119143200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:119137200-119143400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:119137200-119143600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:119137200-119143600	Weak transcription	Lung	lung
47	chr6:119137200-119143600	Weak transcription	Thymus	Thymus
48	chr6:119137200-119145800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:119137200-119146600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:119137200-119146800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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