Variant report

Variant	rs3861950
Chromosome Location	chr1:173156292-173156293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10127495	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10157163	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10158467	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489267	0.82[JPT][hapmap]
rs10912553	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10912554	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912555	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912556	0.82[JPT][hapmap]
rs10912564	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11811856	0.91[CEU][hapmap]
rs1234313	0.90[LWK][hapmap]
rs16845543	1.00[JPT][hapmap]
rs16845558	1.00[JPT][hapmap]
rs16845585	1.00[JPT][hapmap]
rs4081545	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4090391	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4916311	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4916312	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4916313	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028318	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61826341	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6661173	1.00[JPT][hapmap]
rs6665456	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6676785	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6691738	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7514229	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518045	1.00[JPT][hapmap]
rs7518129	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521390	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525284	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7553711	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3861950	TNFSF18	cis	parietal	SCAN
rs3861950	TNN	cis	parietal	SCAN
rs3861950	FMO1	cis	cerebellum	SCAN
rs3861950	PPP1R2	trans	cerebellum	SCAN
rs3861950	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173132200-173158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:173143000-173159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:173148600-173159200	Weak transcription	Lung	lung
4	chr1:173150200-173159600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:173150600-173157600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:173150600-173157800	Strong transcription	HSMM	muscle
7	chr1:173151000-173156400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:173152000-173159400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:173152200-173158000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:173152400-173158400	Strong transcription	HUVEC	blood vessel
11	chr1:173152600-173156800	Strong transcription	Primary hematopoietic stem cells	blood
12	chr1:173153600-173156400	Strong transcription	HSMMtube	muscle
13	chr1:173153600-173159400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:173153600-173159400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:173153800-173159400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:173154000-173159200	Weak transcription	Left Ventricle	heart
17	chr1:173154200-173159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:173154400-173157200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:173154400-173176200	Weak transcription	Aorta	Aorta
20	chr1:173154800-173164600	Weak transcription	Primary B cells from cord blood	blood
21	chr1:173155400-173158800	Weak transcription	Adipose Nuclei	Adipose
22	chr1:173155400-173159400	Weak transcription	Fetal Stomach	stomach
23	chr1:173155600-173159400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:173155600-173159400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:173155600-173159400	Weak transcription	Spleen	Spleen
26	chr1:173155800-173159600	Weak transcription	Thymus	Thymus
27	chr1:173156000-173159400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:173156000-173159400	Weak transcription	Ovary	ovary
29	chr1:173156000-173159400	Weak transcription	HepG2	liver
30	chr1:173156200-173156600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:173156200-173157400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:173156200-173158400	Weak transcription	Dnd41	blood
33	chr1:173156200-173159400	Weak transcription	Brain Substantia Nigra	brain

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