Variant report

Variant	rs12199955
Chromosome Location	chr6:24531450-24531451
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:24531109-24531505	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24530783..24533712-chr6:24700418..24704307,3	MCF-7	breast:

Variant related genes	Relation type
ALDH5A1	TF binding region
ENSG00000272345	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10456306	0.82[CHB][hapmap]
rs12196913	0.82[CHB][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs12211030	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2817239	0.88[CHB][hapmap]
rs34829630	0.83[ASN][1000 genomes]
rs3903801	0.84[ASW][hapmap];0.80[MEX][hapmap]
rs62400513	0.94[ASN][1000 genomes]
rs809419	0.80[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12199955	MRS2	cis	cerebellum	SCAN
rs12199955	HIST1H3A	cis	cerebellum	SCAN
rs12199955	ZKSCAN4	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496000-24534200	Weak transcription	Gastric	stomach
2	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
3	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
6	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
7	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
8	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:24504400-24534200	Weak transcription	Pancreas	Pancrea
10	chr6:24505400-24534000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:24505800-24534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:24505800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:24507600-24532400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:24507600-24532400	Weak transcription	Fetal Brain Female	brain
15	chr6:24507800-24532400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:24507800-24536800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:24507800-24539200	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:24509400-24545800	Weak transcription	Small Intestine	intestine
19	chr6:24512400-24533000	Weak transcription	Brain Substantia Nigra	brain
20	chr6:24515000-24532200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:24516000-24534200	Weak transcription	Brain Angular Gyrus	brain
22	chr6:24516200-24532400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:24517400-24532600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:24517600-24532200	Weak transcription	Left Ventricle	heart
25	chr6:24518600-24531600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:24518800-24533000	Weak transcription	Spleen	Spleen
27	chr6:24519000-24532200	Weak transcription	Ovary	ovary
28	chr6:24519200-24531800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:24521400-24532800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:24523000-24533000	Weak transcription	Fetal Kidney	kidney
31	chr6:24523000-24534200	Weak transcription	Lung	lung
32	chr6:24523000-24537000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:24523200-24532400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:24523200-24532600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:24523200-24534200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:24523200-24534200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:24523200-24534200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:24523600-24536800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:24525200-24531800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:24525200-24532200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:24525200-24533800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:24525400-24532200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:24526400-24537000	Weak transcription	Primary B cells from cord blood	blood
44	chr6:24528200-24531600	Strong transcription	Fetal Stomach	stomach
45	chr6:24528400-24534200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:24528400-24537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:24528400-24540800	Strong transcription	Liver	Liver
48	chr6:24528600-24532400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:24528600-24534200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:24528800-24534400	Weak transcription	Fetal Brain Male	brain

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