Variant report

Variant	rs6550306
Chromosome Location	chr3:34898125-34898126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12053892	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1357428	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474299	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17032340	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17032385	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2071488	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4549234	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4575830	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4678716	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4678717	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678724	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56235912	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58778451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59750319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260224	0.86[ASN][1000 genomes]
rs6792813	0.92[ASN][1000 genomes]
rs73061969	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs73063843	0.82[ASN][1000 genomes]
rs7625986	0.84[ASN][1000 genomes]
rs940047	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv834654	chr3:34747802-34916657	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv834655	chr3:34752929-34898824	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3415700	chr3:34806371-34914306	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv432407	chr3:34869616-34898125	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6550306	SLC22A14	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34896400-34898200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:34896600-34898600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:34897000-34898400	Enhancers	Fetal Muscle Leg	muscle
4	chr3:34897000-34898400	Enhancers	Fetal Thymus	thymus
5	chr3:34897000-34898800	Enhancers	Fetal Heart	heart
6	chr3:34897400-34898200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:34897400-34898400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:34897400-34898600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:34897400-34898600	Enhancers	Fetal Brain Male	brain
10	chr3:34897400-34898600	Enhancers	Dnd41	blood
11	chr3:34897400-34899000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:34897400-34900600	Enhancers	Fetal Intestine Large	intestine
13	chr3:34897600-34898200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:34897600-34898200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:34897600-34898200	Enhancers	Thymus	Thymus
16	chr3:34897600-34898800	Enhancers	Fetal Lung	lung
17	chr3:34897800-34898200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:34897800-34898200	Enhancers	Left Ventricle	heart
19	chr3:34897800-34898200	Enhancers	Psoas Muscle	Psoas
20	chr3:34897800-34898400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:34897800-34898400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:34897800-34898400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:34897800-34898400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:34897800-34898400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:34897800-34898600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:34897800-34898600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:34897800-34898800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:34897800-34899200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:34897800-34899400	Enhancers	Fetal Intestine Small	intestine
30	chr3:34898000-34898400	Enhancers	Primary T cells from cord blood	blood
31	chr3:34898000-34898400	Weak transcription	Fetal Brain Female	brain

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