Variant report

Variant	rs7552939
Chromosome Location	chr1:173767443-173767444
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173767085..173770126-chr1:173792491..173795872,3	K562	blood:
2	chr1:173765333..173767608-chr1:173792402..173794496,2	K562	blood:
3	chr1:173765730..173768496-chr1:173770515..173773260,2	MCF-7	breast:
4	chr1:173763904..173766406-chr1:173767002..173768765,2	K562	blood:
5	chr1:173765402..173769315-chr1:173795358..173797976,3	K562	blood:

Variant related genes	Relation type
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10798295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912656	0.91[CHB][hapmap]
rs10912660	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10912671	0.92[ASW][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap]
rs10912676	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057778	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12067170	0.81[AFR][1000 genomes]
rs12071594	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12071663	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12075071	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12092383	0.85[ASW][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.81[AFR][1000 genomes]
rs1322770	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1322775	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1322777	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1322780	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1799876	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs2065171	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2144708	0.92[ASW][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4606360	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652229	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57592568	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs5877	0.83[ASW][hapmap];0.95[TSI][hapmap]
rs5878	0.83[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6413827	0.81[MEX][hapmap]
rs6425254	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6663875	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6696680	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7515721	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7542910	0.81[AFR][1000 genomes]
rs7544605	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9286895	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs941989	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes]
rs9425416	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9425430	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9425435	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9425745	0.81[MEX][hapmap]
rs9425755	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9425765	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9425766	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9661233	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs969029	0.81[AFR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7552939	SNORD78	cis	parietal	SCAN
rs7552939	TNFSF18	cis	parietal	SCAN
rs7552939	SLC9A11	cis	parietal	SCAN
rs7552939	DARS2	cis	cerebellum	SCAN
rs7552939	PRDX6	cis	parietal	SCAN
rs7552939	CENPL	cis	lymphoblastoid	seeQTL
rs7552939	GPR52	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173729800-173781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:173735800-173781000	Weak transcription	Small Intestine	intestine
3	chr1:173736600-173792400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:173744800-173790200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:173745000-173792400	Weak transcription	Psoas Muscle	Psoas
6	chr1:173747800-173769200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:173749200-173792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:173749800-173777800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:173751200-173773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:173751400-173769000	Weak transcription	Fetal Intestine Small	intestine
11	chr1:173751400-173792200	Weak transcription	Fetal Kidney	kidney
12	chr1:173751800-173774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:173752600-173790000	Weak transcription	HepG2	liver
14	chr1:173752800-173771800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:173752800-173777000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:173753200-173774400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:173753200-173792200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:173753200-173792800	Weak transcription	Esophagus	oesophagus
19	chr1:173753400-173772200	Weak transcription	Aorta	Aorta
20	chr1:173753400-173774400	Weak transcription	Ovary	ovary
21	chr1:173753400-173775000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:173753400-173787800	Weak transcription	Right Ventricle	heart
23	chr1:173753400-173792600	Weak transcription	Spleen	Spleen
24	chr1:173753400-173792800	Weak transcription	Gastric	stomach
25	chr1:173753400-173792800	Weak transcription	Pancreas	Pancrea
26	chr1:173753600-173787600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:173753600-173792600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:173753800-173767800	Weak transcription	A549	lung
29	chr1:173754000-173774400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:173754000-173774600	Weak transcription	Brain Anterior Caudate	brain
31	chr1:173754200-173792200	Weak transcription	Fetal Brain Female	brain
32	chr1:173754400-173774800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:173754400-173782200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:173754400-173786000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:173754400-173792600	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:173755000-173772200	Weak transcription	Left Ventricle	heart
37	chr1:173755200-173791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:173755400-173767800	Weak transcription	NH-A	brain
39	chr1:173755400-173769200	Weak transcription	Primary B cells from cord blood	blood
40	chr1:173755400-173772000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:173755400-173772000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:173755400-173772000	Weak transcription	Fetal Lung	lung
43	chr1:173755400-173772600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:173755400-173774800	Weak transcription	NHLF	lung
45	chr1:173755400-173783200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:173755400-173787400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:173755400-173787400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:173755400-173792200	Weak transcription	HSMMtube	muscle
49	chr1:173755400-173792600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:173756800-173783400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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