Variant report

Variant	rs9850413
Chromosome Location	chr3:119224587-119224588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119219516..119223386-chr3:119224346..119229091,6	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11539377	0.89[YRI][hapmap]
rs11707612	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11709468	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714738	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714843	0.92[ASN][1000 genomes]
rs11719448	0.91[ASN][1000 genomes]
rs11720158	0.91[ASN][1000 genomes]
rs11720423	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916272	0.89[YRI][hapmap]
rs11916344	0.89[YRI][hapmap]
rs11925305	0.89[YRI][hapmap]
rs1599795	0.91[ASN][1000 genomes]
rs1599796	0.91[ASN][1000 genomes]
rs17203188	0.95[CEU][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1938	1.00[CEU][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961132	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049500	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276713	0.91[ASN][1000 genomes]
rs2280670	0.93[ASN][1000 genomes]
rs2293371	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34090996	0.87[ASN][1000 genomes]
rs3732418	0.91[ASN][1000 genomes]
rs3755579	0.95[CEU][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4447803	0.95[CEU][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4461452	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687863	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688009	0.93[ASN][1000 genomes]
rs4688011	0.91[ASN][1000 genomes]
rs4688013	0.91[ASN][1000 genomes]
rs57506457	0.86[ASN][1000 genomes]
rs59024323	0.93[ASN][1000 genomes]
rs60938951	0.83[ASN][1000 genomes]
rs62263444	0.89[ASN][1000 genomes]
rs62264483	0.91[ASN][1000 genomes]
rs62264487	0.91[ASN][1000 genomes]
rs6438534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775021	0.90[YRI][hapmap]
rs6788474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808654	0.89[YRI][hapmap]
rs7610335	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642119	0.89[YRI][hapmap]
rs9289131	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9832341	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869760	0.88[AFR][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	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9850413	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119218000-119225000	Weak transcription	Gastric	stomach
2	chr3:119218000-119231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
4	chr3:119218600-119224600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:119218600-119225000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:119218600-119225000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:119218600-119225000	Weak transcription	Lung	lung
8	chr3:119218600-119231800	Weak transcription	Spleen	Spleen
9	chr3:119218600-119234400	Weak transcription	Colonic Mucosa	Colon
10	chr3:119218600-119236600	Weak transcription	Esophagus	oesophagus
11	chr3:119218800-119225000	Weak transcription	Thymus	Thymus
12	chr3:119218800-119233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:119219000-119224600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:119219000-119235800	Weak transcription	Fetal Kidney	kidney
15	chr3:119219400-119236800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:119219600-119237000	Weak transcription	Small Intestine	intestine
17	chr3:119219800-119224600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:119219800-119228000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr3:119219800-119231000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:119219800-119232000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:119219800-119232000	Weak transcription	Brain Substantia Nigra	brain
22	chr3:119219800-119233600	Weak transcription	Ovary	ovary
23	chr3:119219800-119235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:119219800-119239200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:119220000-119224600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:119220000-119225000	Weak transcription	Pancreas	Pancrea
27	chr3:119220000-119226400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:119220000-119226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:119220000-119226600	Weak transcription	HSMMtube	muscle
30	chr3:119220000-119231800	Weak transcription	Fetal Brain Male	brain
31	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:119220200-119226600	Weak transcription	Psoas Muscle	Psoas
33	chr3:119220200-119228200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:119220200-119229200	Weak transcription	HepG2	liver
35	chr3:119220200-119231800	Weak transcription	Fetal Heart	heart
36	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
37	chr3:119220400-119226200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:119220400-119226800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:119220600-119225000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:119220600-119225600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:119220600-119225600	Strong transcription	Osteobl	bone
42	chr3:119220600-119228400	Strong transcription	Fetal Thymus	thymus
43	chr3:119220600-119230600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:119220800-119224600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:119220800-119225000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:119220800-119225200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:119220800-119226000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:119220800-119228000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:119220800-119243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:119221000-119231000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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