Variant report

Variant	rs556141
Chromosome Location	chr12:40423992-40423993
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1482283	0.80[EUR][1000 genomes]
rs2404347	0.81[ASW][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs4611275	0.81[ASW][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs483163	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs515205	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs515291	0.87[ASW][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs520138	0.94[YRI][hapmap]
rs532802	0.95[CEU][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs549727	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs551739	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556227	1.00[JPT][hapmap]
rs561057	0.93[ASW][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs567779	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs568483	0.93[ASW][hapmap];0.89[LWK][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs569631	0.94[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs556141	TAB3	trans	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:40405400-40445200	Weak transcription	K562	blood
4	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
6	chr12:40406600-40425800	Weak transcription	Liver	Liver
7	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:40411600-40424000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:40411600-40425600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
14	chr12:40411800-40425200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:40411800-40425600	Weak transcription	Fetal Intestine Large	intestine
16	chr12:40411800-40425600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
18	chr12:40415000-40426000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:40416200-40425400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:40416600-40425400	Weak transcription	Psoas Muscle	Psoas
21	chr12:40416600-40441800	Weak transcription	Ovary	ovary
22	chr12:40417000-40426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:40417000-40426400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:40417200-40425200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:40417200-40425400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:40417200-40425600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:40419000-40428600	Weak transcription	Aorta	Aorta
28	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
29	chr12:40420800-40426000	Weak transcription	Fetal Kidney	kidney
30	chr12:40421600-40427000	Weak transcription	Brain Anterior Caudate	brain
31	chr12:40421600-40428000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
33	chr12:40421800-40427800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:40423400-40426000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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