Variant report

Variant	rs16875619
Chromosome Location	chr5:5487311-5487312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:5480560..5482394-chr5:5485667..5488011,2	K562	blood:
2	chr5:5484167..5485806-chr5:5486367..5488712,2	K562	blood:
3	chr5:5485902..5487652-chr5:5492681..5494252,2	K562	blood:
4	chr5:5485235..5487622-chr5:5487665..5490787,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10462631	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16875568	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16875578	0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16875584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16875589	0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16875590	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16875597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16875609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs16875617	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16875618	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16900246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16900247	0.81[EUR][1000 genomes]
rs2306349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35190184	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806873	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3806874	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4283757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4701700	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4702268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4702269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4702270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702271	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72646678	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs728079	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73736664	1.00[EUR][1000 genomes]
rs7713294	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713609	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7714569	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv2757981	chr5:5447098-5764620	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv2759319	chr5:5447098-5764620	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16875619	SH2D2A	trans	brain	seeQTL
rs16875619	GUCA1C	trans	brain	seeQTL
rs16875619	LRTM1	trans	brain	seeQTL
rs16875619	TTR	trans	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:5458600-5495000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:5462400-5494600	Weak transcription	Colonic Mucosa	Colon
4	chr5:5463000-5493800	Weak transcription	Fetal Heart	heart
5	chr5:5465200-5493800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:5465200-5495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:5467600-5488800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:5468000-5494000	Weak transcription	Fetal Brain Male	brain
9	chr5:5470400-5492600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:5472800-5490600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:5475400-5492400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:5475400-5494000	Weak transcription	Fetal Intestine Small	intestine
13	chr5:5475400-5495000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:5476000-5490000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:5476000-5490800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:5476200-5488000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:5476800-5492600	Weak transcription	A549	lung
18	chr5:5477000-5487400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:5477000-5490800	Weak transcription	Esophagus	oesophagus
20	chr5:5477000-5492600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:5477000-5494000	Weak transcription	Psoas Muscle	Psoas
22	chr5:5477000-5494200	Weak transcription	Fetal Kidney	kidney
23	chr5:5477000-5494400	Weak transcription	Small Intestine	intestine
24	chr5:5477000-5494400	Weak transcription	NHLF	lung
25	chr5:5477000-5494600	Weak transcription	Right Ventricle	heart
26	chr5:5477200-5493800	Weak transcription	NHDF-Ad	bronchial
27	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
28	chr5:5477400-5487800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:5478400-5487800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:5478800-5489200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:5479000-5492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:5481000-5489800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:5481000-5490600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:5481000-5491200	Strong transcription	Adipose Nuclei	Adipose
35	chr5:5481000-5491400	Strong transcription	Dnd41	blood
36	chr5:5481200-5487800	Weak transcription	Fetal Lung	lung
37	chr5:5481200-5494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:5481400-5491400	Strong transcription	Hela-S3	cervix
39	chr5:5481600-5489200	Weak transcription	Thymus	Thymus
40	chr5:5481600-5489400	Weak transcription	GM12878-XiMat	blood
41	chr5:5482000-5489200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:5482000-5489200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:5482000-5492400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr5:5482000-5494000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:5482000-5494000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:5482000-5494200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:5482200-5489200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:5482200-5494000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:5482200-5495000	Weak transcription	NHEK	skin
50	chr5:5482400-5491400	Strong transcription	Primary T cells from cord blood	blood

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