Variant report

Variant	rs3769858
Chromosome Location	chr2:179667806-179667807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11693372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12464151	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12465459	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12469367	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12471428	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992014	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13006510	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844334	1.00[ASN][1000 genomes]
rs2366912	0.87[ASN][1000 genomes]
rs6715406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715901	1.00[ASW][hapmap];0.92[YRI][hapmap]
rs6729746	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561149	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591782	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7592323	0.87[ASN][1000 genomes]
rs7600330	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3769858	TTC30B	cis	parietal	SCAN
rs3769858	TTN	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:179610800-179671400	Weak transcription	Ovary	ovary
3	chr2:179639000-179672000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:179639400-179671400	Weak transcription	Gastric	stomach
5	chr2:179646000-179684800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:179647800-179672000	Weak transcription	Fetal Thymus	thymus
7	chr2:179655800-179670800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:179656200-179668400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:179656800-179674400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:179657800-179668800	Weak transcription	Aorta	Aorta
11	chr2:179659200-179671400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:179659400-179698000	Weak transcription	Primary B cells from cord blood	blood
13	chr2:179659800-179671200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:179660000-179669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:179662400-179669600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:179663200-179669400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:179663800-179668600	Strong transcription	HSMMtube	muscle
18	chr2:179663800-179669800	Strong transcription	Primary T cells from cord blood	blood
19	chr2:179663800-179671200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
20	chr2:179664200-179669600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:179664600-179672000	Weak transcription	Thymus	Thymus
22	chr2:179664800-179670000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
23	chr2:179664800-179673000	Active TSS	Right Atrium	heart
24	chr2:179665400-179668800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:179665600-179668400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:179665600-179668600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:179666000-179668200	Transcr. at gene 5' and 3'	Fetal Heart	heart
28	chr2:179666800-179668000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:179666800-179684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:179667200-179673000	Active TSS	Right Ventricle	heart
31	chr2:179667400-179668800	Weak transcription	Pancreas	Pancrea
32	chr2:179667400-179668800	Weak transcription	Psoas Muscle	Psoas
33	chr2:179667400-179669200	Active TSS	Fetal Muscle Trunk	muscle
34	chr2:179667600-179669200	Weak transcription	HSMM	muscle
35	chr2:179667800-179668800	Active TSS	Fetal Muscle Leg	muscle
36	chr2:179667800-179668800	Weak transcription	Left Ventricle	heart

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