Variant report

Variant	rs3829791
Chromosome Location	chr1:161023353-161023354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161022923..161025927-chr1:161065904..161068194,3	MCF-7	breast:
2	chr1:161021235..161023633-chr1:161088651..161090461,2	K562	blood:

Variant related genes	Relation type
ENSG00000158793	Chromatin interaction
ENSG00000162755	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12728349	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12748157	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073657	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516837	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516839	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774273	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34212386	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3813609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3829791	TSTD1	cis	Artery Tibial	GTEx
rs3829791	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
2	chr1:161016600-161024200	Weak transcription	Right Ventricle	heart
3	chr1:161016600-161028000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:161016800-161029200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:161017000-161024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:161017000-161029400	Strong transcription	Primary T cells from cord blood	blood
7	chr1:161017000-161031600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:161017200-161029200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:161017200-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:161017400-161027400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr1:161017400-161027400	Strong transcription	Dnd41	blood
13	chr1:161017400-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:161017400-161031000	Strong transcription	Thymus	Thymus
15	chr1:161017600-161024000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:161017600-161034400	Strong transcription	Fetal Thymus	thymus
17	chr1:161017800-161024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:161017800-161026200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:161018000-161025800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:161018000-161027400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:161018200-161026800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:161018400-161026000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:161018400-161026400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:161018400-161027400	Strong transcription	GM12878-XiMat	blood
25	chr1:161018600-161024200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:161018600-161032400	Strong transcription	Primary B cells from cord blood	blood
27	chr1:161018600-161033600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:161018800-161028200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:161019000-161026600	Strong transcription	Placenta	Placenta
30	chr1:161019400-161026000	Strong transcription	Spleen	Spleen
31	chr1:161019400-161029400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:161019600-161023400	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:161019800-161025800	Weak transcription	Liver	Liver
34	chr1:161020200-161024200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:161020800-161024600	Strong transcription	Esophagus	oesophagus
36	chr1:161020800-161024800	Strong transcription	Lung	lung
37	chr1:161020800-161027400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:161021000-161025200	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr1:161021400-161026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:161021400-161034000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:161021600-161025000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:161021600-161029400	Weak transcription	Stomach Mucosa	stomach
43	chr1:161021600-161033000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:161021600-161038400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:161022600-161024400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:161022600-161028200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:161022800-161026000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:161022800-161029200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:161022800-161031800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:161023000-161024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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