Variant report

Variant	rs1938
Chromosome Location	chr3:119211867-119211868
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119200434..119202905-chr3:119211856..119213563,2	MCF-7	breast:
2	chr3:119201366..119207142-chr3:119210949..119217240,7	K562	blood:
3	chr3:119201357..119202998-chr3:119210933..119213323,2	MCF-7	breast:
4	chr3:119181522..119184148-chr3:119211730..119214140,2	K562	blood:
5	chr3:119205214..119207939-chr3:119209744..119211906,3	MCF-7	breast:
6	chr3:119207787..119212909-chr3:119213285..119218402,8	K562	blood:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000272662	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11707612	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11709468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714738	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714843	0.89[ASN][1000 genomes]
rs11719448	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11720158	0.87[ASN][1000 genomes]
rs11720423	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599795	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1599796	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs17203104	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17203188	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1961132	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2049500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276713	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2280670	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2293371	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34090996	0.89[ASN][1000 genomes]
rs3732418	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs3755579	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4447803	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4461452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687851	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4687854	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4687863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688002	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4688009	0.90[ASN][1000 genomes]
rs4688011	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4688013	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs57506457	0.87[ASN][1000 genomes]
rs59024323	0.90[ASN][1000 genomes]
rs60938951	0.84[ASN][1000 genomes]
rs62263404	0.81[ASN][1000 genomes]
rs62263406	0.81[ASN][1000 genomes]
rs62263444	0.91[ASN][1000 genomes]
rs62264483	0.87[ASN][1000 genomes]
rs62264487	0.87[ASN][1000 genomes]
rs6438534	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788474	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7610335	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7626731	0.89[YRI][hapmap]
rs9289131	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9832341	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9850413	1.00[CEU][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	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
rs1938	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
6	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
7	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:119189800-119212200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
10	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:119190400-119212200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:119190600-119212000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain
16	chr3:119192400-119216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:119195800-119212000	Strong transcription	Liver	Liver
18	chr3:119196400-119216200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:119196400-119216600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:119196800-119216800	Weak transcription	Small Intestine	intestine
21	chr3:119197000-119216400	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:119197400-119216600	Weak transcription	Aorta	Aorta
23	chr3:119202400-119212000	Strong transcription	Primary T cells from cord blood	blood
24	chr3:119202400-119213800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:119203000-119212000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr3:119204200-119212000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:119204200-119212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:119204400-119212000	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:119204800-119216400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:119205000-119216000	Weak transcription	Fetal Kidney	kidney
31	chr3:119205400-119216400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:119205600-119216600	Weak transcription	Colonic Mucosa	Colon
33	chr3:119205600-119216600	Weak transcription	Esophagus	oesophagus
34	chr3:119205600-119216600	Weak transcription	Gastric	stomach
35	chr3:119205800-119216000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:119205800-119216200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:119205800-119216200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:119205800-119216200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:119205800-119216600	Weak transcription	Pancreas	Pancrea
40	chr3:119205800-119217000	Weak transcription	Spleen	Spleen
41	chr3:119206000-119216200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:119206000-119216200	Weak transcription	Fetal Lung	lung
43	chr3:119206000-119216200	Weak transcription	Psoas Muscle	Psoas
44	chr3:119206000-119216600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:119206200-119216000	Weak transcription	NHLF	lung
46	chr3:119206200-119216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:119206200-119216200	Weak transcription	NH-A	brain
48	chr3:119206400-119216200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:119206800-119216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:119206800-119216200	Weak transcription	Brain Anterior Caudate	brain

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