Variant report

Variant	rs12200498
Chromosome Location	chr6:35685955-35685956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35674895..35677260-chr6:35683574..35687418,3	K562	blood:
2	chr6:35657828..35659372-chr6:35684288..35686533,2	MCF-7	breast:
3	chr6:35654589..35656249-chr6:35685237..35687965,2	K562	blood:
4	chr6:35677736..35680462-chr6:35681912..35686397,4	K562	blood:
5	chr6:35674895..35676594-chr6:35684420..35687418,2	K562	blood:
6	chr6:35681922..35687199-chr6:35692770..35697026,9	MCF-7	breast:
7	chr6:35677094..35679566-chr6:35684897..35686689,2	K562	blood:

Variant related genes	Relation type
ENSG00000096060	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10456432	0.86[CHB][hapmap]
rs10947565	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12193672	0.88[EUR][1000 genomes]
rs12203716	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12206670	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17542466	0.86[CHB][hapmap]
rs45586442	0.90[EUR][1000 genomes]
rs56354119	0.88[EUR][1000 genomes]
rs7752049	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1028947	chr6:35670521-35714541	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv885805	chr6:35685955-35779879	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12200498	C6orf125	cis	cerebellum	SCAN
rs12200498	TBC1D22B	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35678200-35686000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:35678400-35686800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:35679000-35688000	Weak transcription	Pancreas	Pancrea
4	chr6:35680800-35690200	Weak transcription	Gastric	stomach
5	chr6:35683600-35686200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:35683800-35686000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:35683800-35688800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr6:35684000-35686600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:35684000-35687000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:35684000-35688800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:35684200-35686600	Enhancers	Primary T cells from cord blood	blood
12	chr6:35684200-35686600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:35684200-35686800	Enhancers	Fetal Kidney	kidney
14	chr6:35684200-35687800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:35684200-35688600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:35684400-35686600	Weak transcription	Right Ventricle	heart
17	chr6:35684400-35686800	Enhancers	Brain Anterior Caudate	brain
18	chr6:35684400-35687400	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:35684400-35687400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:35684400-35687400	Enhancers	Duodenum Mucosa	Duodenum
21	chr6:35684400-35687600	Enhancers	Fetal Muscle Trunk	muscle
22	chr6:35684400-35687800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr6:35684400-35688600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr6:35684400-35688600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:35684400-35688800	Enhancers	Brain Substantia Nigra	brain
26	chr6:35684600-35686200	Enhancers	Dnd41	blood
27	chr6:35684600-35686800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:35684600-35687200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:35684600-35687600	Enhancers	Fetal Stomach	stomach
30	chr6:35684600-35687800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:35684600-35687800	Enhancers	Adipose Nuclei	Adipose
32	chr6:35684600-35688400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:35684600-35688600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr6:35684600-35688600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:35684600-35688800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:35684800-35687000	Enhancers	Colonic Mucosa	Colon
37	chr6:35685000-35686000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:35685000-35686200	Enhancers	GM12878-XiMat	blood
39	chr6:35685000-35687200	Enhancers	Fetal Heart	heart
40	chr6:35685000-35687400	Enhancers	Brain Hippocampus Middle	brain
41	chr6:35685000-35687400	Enhancers	Fetal Muscle Leg	muscle
42	chr6:35685000-35687800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:35685000-35688000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:35685000-35688600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:35685000-35688800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:35685000-35689000	Enhancers	Lung	lung
47	chr6:35685200-35686400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:35685200-35687400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr6:35685200-35687400	Enhancers	Fetal Lung	lung
50	chr6:35685200-35687600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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