Variant report

Variant	rs2126978
Chromosome Location	chr19:38097006-38097007
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38094621..38097474-chr19:38099198..38101401,2	K562	blood:
2	chr19:38085406..38087433-chr19:38096003..38098088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180479	Chromatin interaction
ENSG00000171817	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1038084	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1038085	0.84[CEU][hapmap]
rs10407657	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10424612	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10425671	0.84[CEU][hapmap]
rs1116234	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668434	0.89[CEU][hapmap]
rs11668558	0.89[CEU][hapmap]
rs11672077	0.89[CEU][hapmap]
rs11883392	0.84[CEU][hapmap]
rs12981750	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17306508	0.89[CEU][hapmap]
rs1871197	0.84[CEU][hapmap]
rs2045909	0.89[CEU][hapmap]
rs2061778	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2160640	0.89[CEU][hapmap]
rs2199644	0.89[CEU][hapmap]
rs241948	0.89[CEU][hapmap]
rs2891683	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2927743	1.00[CHB][hapmap]
rs2927744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972456	0.84[CEU][hapmap]
rs2972459	0.84[CEU][hapmap]
rs3752365	0.84[CEU][hapmap]
rs4482404	0.89[CEU][hapmap]
rs4802069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803216	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803228	0.89[CEU][hapmap]
rs62108344	0.86[EUR][1000 genomes]
rs6508738	0.83[CEU][hapmap]
rs7254170	0.83[CEU][hapmap]
rs7254828	0.89[CEU][hapmap]
rs7255283	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7256747	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7259566	1.00[EUR][1000 genomes]
rs8102916	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8113076	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs856302	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38086600-38098200	Weak transcription	Colonic Mucosa	Colon
2	chr19:38086600-38098800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:38086600-38099400	Weak transcription	Fetal Stomach	stomach
4	chr19:38086600-38103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:38087200-38099400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:38087200-38100200	Weak transcription	Right Ventricle	heart
7	chr19:38087200-38103000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:38087800-38107400	ZNF genes & repeats	Liver	Liver
9	chr19:38089200-38107200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
10	chr19:38090400-38097600	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr19:38090400-38105200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr19:38090600-38105400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr19:38091200-38101000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38092200-38103400	Weak transcription	Thymus	Thymus
15	chr19:38092400-38102400	Weak transcription	Dnd41	blood
16	chr19:38092600-38097200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:38093400-38100200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr19:38093600-38102800	Weak transcription	Fetal Brain Female	brain
19	chr19:38093600-38105000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr19:38093800-38099600	Weak transcription	Pancreas	Pancrea
21	chr19:38093800-38101000	Weak transcription	Psoas Muscle	Psoas
22	chr19:38094200-38097400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:38094200-38098400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:38094200-38098800	Weak transcription	Aorta	Aorta
25	chr19:38094200-38098800	Weak transcription	Lung	lung
26	chr19:38094600-38097200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:38094600-38102600	Weak transcription	Fetal Brain Male	brain
28	chr19:38094600-38103200	Weak transcription	Brain Germinal Matrix	brain
29	chr19:38095400-38097200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:38095400-38099800	Strong transcription	Left Ventricle	heart
31	chr19:38095400-38107200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
32	chr19:38095600-38097600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:38095600-38098400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:38095600-38100000	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr19:38095600-38100000	ZNF genes & repeats	Colon Smooth Muscle	Colon
36	chr19:38095600-38105000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr19:38095600-38105400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:38095800-38097600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:38095800-38098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:38095800-38101000	Weak transcription	Fetal Kidney	kidney
41	chr19:38096000-38099600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:38096400-38097600	Strong transcription	Brain Anterior Caudate	brain
43	chr19:38096600-38097200	ZNF genes & repeats	Brain Hippocampus Middle	brain
44	chr19:38096600-38100400	ZNF genes & repeats	Ovary	ovary
45	chr19:38096800-38097600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:38096800-38097600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
47	chr19:38096800-38099800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
48	chr19:38096800-38099800	ZNF genes & repeats	Brain Substantia Nigra	brain
49	chr19:38096800-38105400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
50	chr19:38097000-38097400	ZNF genes & repeats	Brain Angular Gyrus	brain

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