Variant report

Variant	rs17644324
Chromosome Location	chr6:121526780-121526781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10457413	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10457414	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10457415	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10499106	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10499109	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.82[ASN][1000 genomes]
rs11153999	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11154001	0.86[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11154002	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11154005	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11154011	0.85[EUR][1000 genomes]
rs11154012	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11759795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12191616	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12198421	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12206641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12212646	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13199297	1.00[ASW][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs28877073	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs407630	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7742017	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7745023	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9387918	0.96[CEU][hapmap];1.00[YRI][hapmap]

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	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv604572	chr6:121465011-121544876	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv524172	chr6:121523736-121526898	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17644324	GUCA1B	trans	brain	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121478800-121535400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:121480200-121535600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:121480800-121535400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:121481000-121535400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:121487400-121556000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:121495200-121529400	Weak transcription	Primary B cells from cord blood	blood
7	chr6:121496800-121535400	Weak transcription	Fetal Lung	lung
8	chr6:121498600-121535400	Weak transcription	Pancreas	Pancrea
9	chr6:121499800-121535800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:121500000-121529000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:121502600-121529000	Weak transcription	Left Ventricle	heart
12	chr6:121509600-121575400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:121511400-121535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:121511800-121535400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:121514200-121535600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:121514600-121529400	Weak transcription	Ovary	ovary
17	chr6:121515000-121535800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:121515200-121535400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:121515200-121535400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:121515400-121535400	Weak transcription	Gastric	stomach
21	chr6:121515600-121544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:121515800-121532800	Weak transcription	Fetal Intestine Small	intestine
23	chr6:121516000-121535400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:121516000-121560200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:121516800-121535400	Weak transcription	Esophagus	oesophagus
26	chr6:121517800-121535400	Weak transcription	Aorta	Aorta
27	chr6:121518000-121529000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:121518200-121535400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:121518600-121535400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:121519000-121531800	Weak transcription	Primary T cells from cord blood	blood
31	chr6:121519000-121535600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:121520200-121535400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:121521000-121535400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:121522600-121533000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:121522600-121535400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:121525600-121527000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr6:121526200-121526800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr6:121526200-121534200	Weak transcription	Dnd41	blood
39	chr6:121526400-121527000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr6:121526600-121527000	Enhancers	HUES64 Cell Line	embryonic stem cell

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