Variant report

Variant	rs9289129
Chromosome Location	chr3:119137855-119137856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119137043..119139802-chr3:119141104..119143797,2	K562	blood:
2	chr3:119137603..119139843-chr3:119394787..119396303,2	MCF-7	breast:
3	chr3:119137060..119139008-chr3:119172885..119175851,2	K562	blood:
4	chr3:119130788..119134912-chr3:119135156..119139620,7	K562	blood:

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1060569	0.94[ASN][1000 genomes]
rs13080905	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797839	0.85[ASN][1000 genomes]
rs1900742	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1919586	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1919590	0.98[ASN][1000 genomes]
rs1967621	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1976919	0.94[ASN][1000 genomes]
rs2177812	0.94[ASN][1000 genomes]
rs3732413	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3732419	0.85[YRI][hapmap]
rs3814397	0.85[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4687860	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688005	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688007	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688008	0.94[ASN][1000 genomes]
rs4688012	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4688014	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414282	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414283	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438529	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438530	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438531	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438532	0.82[YRI][hapmap]
rs6438535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6777535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778945	0.87[ASN][1000 genomes]
rs6794822	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796970	0.98[ASN][1000 genomes]
rs6799691	0.86[YRI][hapmap]
rs71618795	0.84[EUR][1000 genomes]
rs727905	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7430798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621259	0.94[ASN][1000 genomes]
rs7628626	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7630587	0.98[ASN][1000 genomes]
rs7642502	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9809155	0.98[ASN][1000 genomes]
rs9836627	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9850447	0.87[ASN][1000 genomes]
rs9867768	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs9873196	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9874480	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9877854	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9289129	KTELC1	cis	multi-tissue	Pritchard
rs9289129	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119080000-119145600	Weak transcription	Fetal Kidney	kidney
2	chr3:119082800-119138000	Weak transcription	Small Intestine	intestine
3	chr3:119085200-119139000	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:119098400-119138200	Strong transcription	Adipose Nuclei	Adipose
5	chr3:119110200-119140800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:119112000-119147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:119112200-119138800	Weak transcription	Colonic Mucosa	Colon
8	chr3:119113200-119140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:119113400-119138000	Strong transcription	Fetal Stomach	stomach
10	chr3:119119000-119138800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:119121200-119150000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:119127200-119138200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:119129000-119138400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:119130200-119139200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:119130600-119138400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:119130800-119143600	Weak transcription	GM12878-XiMat	blood
17	chr3:119132800-119138000	Strong transcription	Lung	lung
18	chr3:119133600-119140400	Weak transcription	NHLF	lung
19	chr3:119133800-119147400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:119134000-119138200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:119134200-119148800	Weak transcription	Pancreas	Pancrea
22	chr3:119134400-119138800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:119134600-119147600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:119134800-119139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:119134800-119147400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:119135000-119139000	Weak transcription	Fetal Intestine Small	intestine
27	chr3:119135000-119139200	Weak transcription	Right Atrium	heart
28	chr3:119135000-119140800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:119135000-119147400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:119135000-119147600	Weak transcription	Fetal Thymus	thymus
31	chr3:119135000-119147800	Weak transcription	Placenta	Placenta
32	chr3:119135000-119148000	Weak transcription	Aorta	Aorta
33	chr3:119135200-119139200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:119135200-119139600	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:119135200-119139800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:119135200-119140800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:119135200-119145000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:119135200-119149800	Weak transcription	Gastric	stomach
39	chr3:119135400-119139000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:119135400-119139000	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:119135400-119145600	Weak transcription	HUVEC	blood vessel
42	chr3:119135400-119147800	Weak transcription	Ovary	ovary
43	chr3:119135400-119148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:119135400-119150000	Weak transcription	Spleen	Spleen
45	chr3:119135600-119139200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:119136600-119138000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:119136800-119138000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:119136800-119139000	Weak transcription	Right Ventricle	heart
49	chr3:119136800-119145600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:119137000-119138000	Enhancers	HSMM	muscle

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