Variant report

Variant	rs12208087
Chromosome Location	chr6:38559489-38559490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38549497..38552330-chr6:38556506..38559502,2	K562	blood:
2	chr6:38554358..38556905-chr6:38558804..38560728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217227	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10484854	1.00[CHB][hapmap]
rs10484856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073900	0.92[CEU][hapmap]
rs10947749	0.92[CEU][hapmap]
rs10947750	0.92[CEU][hapmap]
rs12154188	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193868	0.92[CEU][hapmap];1.00[AFR][1000 genomes]
rs12198212	1.00[CHB][hapmap]
rs12198294	0.92[CEU][hapmap]
rs12199427	0.87[CEU][hapmap];1.00[AFR][1000 genomes]
rs12206218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206371	0.92[CEU][hapmap]
rs12214815	0.82[CHB][hapmap]
rs1406841	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699015	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699018	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17543429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622097	0.82[CHB][hapmap]
rs1781742	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1937780	0.82[CHB][hapmap]
rs28616055	1.00[AFR][1000 genomes]
rs4074421	0.88[CEU][hapmap];1.00[AFR][1000 genomes]
rs4254983	0.92[CEU][hapmap]
rs55869483	1.00[AFR][1000 genomes]
rs6458060	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927145	0.95[CEU][hapmap]
rs72853429	1.00[AFR][1000 genomes]
rs72856516	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7743871	0.88[CEU][hapmap]
rs7752239	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755619	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767041	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
2	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung
4	chr6:38535800-38560200	Weak transcription	NH-A	brain
5	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:38536400-38560200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
9	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
10	chr6:38538600-38561800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:38538600-38562000	Weak transcription	Brain Germinal Matrix	brain
12	chr6:38539800-38562800	Weak transcription	Fetal Thymus	thymus
13	chr6:38540400-38560000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:38540400-38561600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:38540400-38567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:38540400-38569200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:38540600-38560000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:38541000-38565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:38541400-38568600	Weak transcription	Spleen	Spleen
20	chr6:38541600-38567000	Weak transcription	Small Intestine	intestine
21	chr6:38542000-38563400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:38542800-38560200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:38543400-38560200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:38544400-38560000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:38545000-38561400	Weak transcription	Psoas Muscle	Psoas
26	chr6:38545400-38566000	Weak transcription	Colonic Mucosa	Colon
27	chr6:38546200-38563800	Weak transcription	Gastric	stomach
28	chr6:38546600-38559800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:38547400-38560000	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:38547400-38565400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:38547400-38566600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:38547600-38559800	Weak transcription	Brain Anterior Caudate	brain
33	chr6:38548200-38559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:38548200-38559800	Weak transcription	Left Ventricle	heart
35	chr6:38548200-38559800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:38548200-38561600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:38548200-38563800	Weak transcription	Brain Substantia Nigra	brain
38	chr6:38548200-38570800	Weak transcription	Fetal Kidney	kidney
39	chr6:38548400-38560000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:38549000-38570800	Weak transcription	Fetal Intestine Small	intestine
41	chr6:38553400-38562200	Strong transcription	Primary T cells from cord blood	blood
42	chr6:38554600-38560000	Weak transcription	Fetal Brain Female	brain
43	chr6:38555000-38565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:38556000-38559600	Weak transcription	Fetal Intestine Large	intestine
45	chr6:38556000-38560200	Weak transcription	Aorta	Aorta
46	chr6:38556000-38560200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:38556000-38563800	Weak transcription	Fetal Heart	heart
48	chr6:38556000-38580400	Weak transcription	Ovary	ovary
49	chr6:38556200-38559600	Weak transcription	Fetal Stomach	stomach
50	chr6:38556200-38559800	Weak transcription	Brain Inferior Temporal Lobe	brain

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