Variant report

Variant	rs7290317
Chromosome Location	chr22:30808561-30808562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30804147..30805729-chr22:30808018..30809616,2	K562	blood:
2	chr22:30800645..30802229-chr22:30805935..30808641,2	MCF-7	breast:
3	chr22:30807917..30810570-chr22:30811871..30814517,2	K562	blood:

Variant related genes	Relation type
ENSG00000100003	Chromatin interaction
ENSG00000268538	Chromatin interaction
ENSG00000249590	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1010324	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11089442	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs11089447	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11089448	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11089449	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11703867	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11705639	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12171261	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072160	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2267154	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267155	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267156	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283866	0.81[AMR][1000 genomes]
rs2283870	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283871	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299827	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839998	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57940170	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5994294	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5994305	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5994306	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997637	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997646	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61583714	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71331235	0.82[AMR][1000 genomes]
rs7288366	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7289360	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9619096	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs9619098	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9619105	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9620984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7290317	SEC14L3	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
3	chr22:30794400-30811800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:30794600-30811400	Weak transcription	Right Ventricle	heart
5	chr22:30794800-30811400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr22:30794800-30811600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
8	chr22:30795000-30809800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr22:30795000-30814600	Weak transcription	Colon Smooth Muscle	Colon
10	chr22:30795200-30809000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr22:30795200-30810200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30795200-30811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:30795200-30814400	Weak transcription	Small Intestine	intestine
14	chr22:30795400-30812000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr22:30796000-30813400	Weak transcription	Fetal Kidney	kidney
16	chr22:30796200-30811400	Weak transcription	Placenta	Placenta
17	chr22:30797800-30816400	Strong transcription	Dnd41	blood
18	chr22:30798600-30811400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr22:30798600-30811600	Weak transcription	GM12878-XiMat	blood
20	chr22:30798600-30812000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr22:30798600-30812200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:30798800-30811400	Weak transcription	Colonic Mucosa	Colon
23	chr22:30799400-30812000	Weak transcription	Stomach Mucosa	stomach
24	chr22:30799400-30817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr22:30800200-30812600	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr22:30800600-30811600	Weak transcription	Psoas Muscle	Psoas
27	chr22:30801200-30814400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr22:30801400-30816600	Strong transcription	Fetal Stomach	stomach
29	chr22:30801800-30810000	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr22:30802000-30816400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr22:30802200-30816200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr22:30802200-30817000	Genic enhancers	Liver	Liver
33	chr22:30802400-30811600	Strong transcription	Fetal Intestine Small	intestine
34	chr22:30802400-30811800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr22:30802600-30811400	Weak transcription	Adipose Nuclei	Adipose
36	chr22:30802600-30811800	Strong transcription	Fetal Intestine Large	intestine
37	chr22:30802600-30814800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr22:30803200-30809400	Strong transcription	Esophagus	oesophagus
39	chr22:30803200-30814000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:30803200-30817200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr22:30803400-30811600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr22:30803400-30815200	Strong transcription	Brain Substantia Nigra	brain
43	chr22:30803600-30811400	Weak transcription	Spleen	Spleen
44	chr22:30803600-30812000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr22:30804000-30810600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr22:30804400-30808600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr22:30804800-30815600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr22:30805000-30810800	Weak transcription	Fetal Brain Male	brain
49	chr22:30805000-30811600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr22:30805000-30811600	Weak transcription	Aorta	Aorta

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