Variant report

Variant	rs12198838
Chromosome Location	chr6:16639979-16639980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10807595	0.81[EUR][1000 genomes]
rs10949371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949372	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197334	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs12203546	0.80[EUR][1000 genomes]
rs12211723	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524527	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603856	0.86[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17667167	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2092299	0.81[EUR][1000 genomes]
rs2143067	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62387972	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs729769	0.81[EUR][1000 genomes]
rs729770	0.84[CEU][hapmap];0.81[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	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16584000-16670000	Weak transcription	Fetal Brain Male	brain
2	chr6:16585400-16644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:16592600-16645000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:16606000-16653200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:16622200-16651400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:16626000-16644200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:16626200-16654000	Weak transcription	Fetal Kidney	kidney
8	chr6:16627400-16641200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:16627800-16652000	Weak transcription	Thymus	Thymus
10	chr6:16629000-16653400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:16629200-16644400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:16629800-16641200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:16630800-16644800	Weak transcription	Lung	lung
14	chr6:16631000-16641000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:16631600-16641400	Weak transcription	Fetal Brain Female	brain
16	chr6:16632000-16652000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:16634400-16644800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:16634400-16651400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:16634400-16653200	Weak transcription	Fetal Heart	heart
20	chr6:16634600-16640200	Weak transcription	Primary T cells from cord blood	blood
21	chr6:16634600-16645000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:16634600-16648200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:16636000-16641200	Weak transcription	Fetal Lung	lung
24	chr6:16636400-16653400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:16636600-16645000	Weak transcription	Liver	Liver
26	chr6:16636800-16640000	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:16636800-16640200	Weak transcription	Brain Substantia Nigra	brain
28	chr6:16636800-16641200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:16636800-16642200	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:16636800-16644800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:16636800-16645200	Weak transcription	Ovary	ovary
32	chr6:16636800-16646800	Weak transcription	Pancreas	Pancrea
33	chr6:16636800-16650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:16636800-16651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:16636800-16652000	Weak transcription	Aorta	Aorta
36	chr6:16636800-16652200	Weak transcription	Psoas Muscle	Psoas
37	chr6:16636800-16652800	Weak transcription	Esophagus	oesophagus
38	chr6:16636800-16652800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:16636800-16653400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:16636800-16653400	Weak transcription	Left Ventricle	heart
41	chr6:16636800-16653400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:16636800-16653400	Weak transcription	Spleen	Spleen
43	chr6:16636800-16653600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:16636800-16658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:16636800-16661800	Weak transcription	Right Ventricle	heart
46	chr6:16636800-16667400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:16636800-16669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:16636800-16672600	Weak transcription	Gastric	stomach
49	chr6:16637000-16640000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:16637000-16640000	Weak transcription	Hela-S3	cervix

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