Variant report

Variant	rs4916358
Chromosome Location	chr1:173423799-173423800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173423508..173426333-chr1:173427997..173430407,3	K562	blood:
2	chr1:173422565..173425228-chr1:173444418..173448207,4	K562	blood:
3	chr1:173419821..173425727-chr1:173444702..173448978,9	MCF-7	breast:
4	chr1:173422573..173424450-chr1:173433493..173435623,2	K562	blood:
5	chr1:173422794..173425781-chr1:173831369..173833228,2	MCF-7	breast:
6	chr1:173422729..173424426-chr1:173445617..173447163,2	MCF-7	breast:
7	chr1:173422699..173424589-chr1:173837252..173839169,2	K562	blood:
8	chr1:173414044..173416601-chr1:173422234..173425092,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270084	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10753081	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798282	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912656	0.82[CHB][hapmap]
rs12092383	0.81[CHB][hapmap]
rs12140760	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1359460	0.81[LWK][hapmap]
rs4255417	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4276950	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4325171	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4382766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611	0.84[ASN][1000 genomes]
rs4916220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916355	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916359	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916361	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916362	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916363	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55654074	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425231	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6696012	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702835	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7314	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs7537938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540065	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7556003	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425723	0.92[ASN][1000 genomes]
rs9425724	0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4916358	TNFSF4	cis	parietal	SCAN
rs4916358	FASLG	cis	cerebellum	SCAN
rs4916358	PRDX6	cis	cerebellum	SCAN
rs4916358	SLC9A11	cis	parietal	SCAN
rs4916358	PRDX6	cis	parietal	SCAN
rs4916358	GPR52	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173376200-173429000	Weak transcription	Gastric	stomach
2	chr1:173387600-173429000	Weak transcription	Lung	lung
3	chr1:173391800-173429000	Weak transcription	Ovary	ovary
4	chr1:173399400-173424200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:173400400-173429000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:173400600-173428800	Weak transcription	Fetal Stomach	stomach
7	chr1:173400800-173429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:173400800-173429000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:173401000-173428800	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:173401000-173429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:173401000-173429000	Weak transcription	Left Ventricle	heart
12	chr1:173401800-173429000	Weak transcription	Primary B cells from cord blood	blood
13	chr1:173404200-173429000	Weak transcription	Adipose Nuclei	Adipose
14	chr1:173404200-173429000	Weak transcription	Right Ventricle	heart
15	chr1:173408800-173429000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:173408800-173429000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:173409000-173428800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:173409000-173428800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:173409000-173429200	Weak transcription	Aorta	Aorta
20	chr1:173411400-173427000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:173411600-173428800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:173413400-173429200	Weak transcription	Placenta	Placenta
23	chr1:173414600-173429000	Weak transcription	Thymus	Thymus
24	chr1:173415000-173424200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:173415000-173424200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:173415600-173429000	Weak transcription	Brain Angular Gyrus	brain
27	chr1:173416000-173429000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:173416200-173424400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:173416200-173429000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:173416400-173429000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:173416400-173430000	Weak transcription	Fetal Lung	lung
32	chr1:173416600-173429400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:173416800-173424200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:173416800-173429000	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:173416800-173430000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:173416800-173430200	Weak transcription	GM12878-XiMat	blood
37	chr1:173417400-173424200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:173418800-173429000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:173418800-173429000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:173418800-173429000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:173419000-173429000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:173419000-173429200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:173419000-173432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:173419000-173439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:173419200-173428800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:173419400-173429000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:173419800-173429000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:173421000-173423800	Strong transcription	Primary T cells from cord blood	blood
49	chr1:173421000-173432200	Weak transcription	Fetal Brain Male	brain
50	chr1:173421400-173429000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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