Variant report

Variant	rs6682435
Chromosome Location	chr1:193144503-193144504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16835169	0.83[AMR][1000 genomes]
rs16835204	1.00[MEX][hapmap]
rs56067713	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58056953	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6665739	0.83[AMR][1000 genomes]
rs6665751	0.83[AMR][1000 genomes]
rs6683844	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6687899	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap]
rs74130921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130925	0.83[AMR][1000 genomes]
rs74130927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130929	0.83[AMR][1000 genomes]
rs74130930	0.83[AMR][1000 genomes]
rs74130931	1.00[AFR][1000 genomes]
rs7522932	1.00[MEX][hapmap]
rs7531808	0.87[AFR][1000 genomes]
rs7553830	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap]
rs7556154	1.00[MEX][hapmap]
rs7556241	1.00[MEX][hapmap]

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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv832148	chr1:193143945-193292897	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6682435	CD3D	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193094800-193155000	Weak transcription	Aorta	Aorta
2	chr1:193110000-193149400	Weak transcription	Right Ventricle	heart
3	chr1:193110000-193155200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:193116600-193149400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:193118000-193147800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:193120400-193150400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:193121000-193155200	Weak transcription	Pancreas	Pancrea
8	chr1:193123200-193147400	Weak transcription	Fetal Brain Female	brain
9	chr1:193123200-193151600	Weak transcription	Fetal Kidney	kidney
10	chr1:193123200-193153600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:193123400-193147600	Weak transcription	Fetal Brain Male	brain
12	chr1:193123400-193155200	Weak transcription	Thymus	Thymus
13	chr1:193123600-193149600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:193123800-193147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:193123800-193150400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:193123800-193153200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:193124000-193152000	Weak transcription	Liver	Liver
18	chr1:193124000-193153600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:193124000-193154200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:193124200-193150400	Weak transcription	NHDF-Ad	bronchial
21	chr1:193125200-193152200	Weak transcription	A549	lung
22	chr1:193126200-193147800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:193126200-193152600	Weak transcription	HepG2	liver
24	chr1:193126200-193154400	Weak transcription	NHEK	skin
25	chr1:193126200-193155200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:193126200-193155200	Weak transcription	Gastric	stomach
27	chr1:193126400-193147800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:193126800-193155000	Weak transcription	Fetal Thymus	thymus
29	chr1:193127600-193154400	Weak transcription	Hela-S3	cervix
30	chr1:193128600-193154800	Weak transcription	NH-A	brain
31	chr1:193128800-193150200	Weak transcription	Osteobl	bone
32	chr1:193129400-193153600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:193130400-193147600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:193130400-193147600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:193130400-193154800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:193130600-193147000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:193131800-193158600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:193133200-193153600	Weak transcription	Fetal Intestine Small	intestine
39	chr1:193133200-193154800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:193133200-193154800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:193134000-193154400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:193135600-193155000	Weak transcription	Small Intestine	intestine
43	chr1:193135600-193155200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:193136000-193149400	Weak transcription	Left Ventricle	heart
45	chr1:193136000-193152600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:193136000-193152600	Weak transcription	Fetal Stomach	stomach
47	chr1:193137600-193150400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:193137600-193154400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:193137600-193154800	Weak transcription	HMEC	breast
50	chr1:193137800-193145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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