Variant report

Variant	rs3742193
Chromosome Location	chr13:111280002-111280003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111265898..111273230-chr13:111273500..111281065,16	MCF-7	breast:
2	chr13:111278124..111281264-chr13:111364873..111369262,5	MCF-7	breast:
3	chr13:111266306..111273367-chr13:111274094..111280494,12	K562	blood:
4	chr13:111277332..111280156-chr13:111289105..111290945,2	MCF-7	breast:
5	chr13:111266604..111270536-chr13:111275017..111281975,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213995	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1041143	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1041173	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11069855	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11069856	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620520	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12428965	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429905	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12430333	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583083	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1853860	0.89[JPT][hapmap]
rs1853861	0.90[JPT][hapmap]
rs2011692	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148081	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274411	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296659	0.89[JPT][hapmap]
rs28384426	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3742194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783097	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825465	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825466	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825467	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238278	0.81[JPT][hapmap]
rs4628819	0.81[JPT][hapmap]
rs4771700	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4771701	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4771702	0.90[JPT][hapmap]
rs4771703	0.90[JPT][hapmap]
rs4771704	0.90[JPT][hapmap]
rs4773230	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773232	0.90[JPT][hapmap]
rs61103246	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72661645	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661647	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661650	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661656	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72661657	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328764	0.81[JPT][hapmap]
rs7335538	0.81[JPT][hapmap]
rs7336283	0.81[JPT][hapmap]
rs7981194	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981780	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7993933	0.89[JPT][hapmap]
rs7995119	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9583518	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9583520	0.90[JPT][hapmap]
rs9588207	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9588209	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9588214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
14	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
18	nsv456120	chr13:111280002-111309617	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
19	nsv563125	chr13:111280002-111309617	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3742193	CARKD	cis	cerebellum	SCAN
rs3742193	PCID2	cis	cerebellum	SCAN
rs3742193	TNFSF13B	cis	cerebellum	SCAN
rs3742193	CARKD	cis	parietal	SCAN
rs3742193	GRTP1	cis	cerebellum	SCAN
rs3742193	TUBGCP3	cis	parietal	SCAN
rs3742193	AL139385.1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:111269400-111286600	Weak transcription	Fetal Brain Male	brain
3	chr13:111269400-111287200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr13:111270400-111280200	Weak transcription	Fetal Heart	heart
5	chr13:111270400-111282800	Weak transcription	Fetal Kidney	kidney
6	chr13:111270800-111296800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:111271200-111287000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr13:111271400-111281400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:111271600-111281600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:111273400-111281200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr13:111274400-111284400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr13:111274600-111281200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr13:111274600-111281400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:111274600-111281600	Strong transcription	Brain Anterior Caudate	brain
15	chr13:111274600-111281800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr13:111274600-111282200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:111274600-111282200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:111274600-111282400	Strong transcription	NHLF	lung
19	chr13:111274600-111283600	Strong transcription	Thymus	Thymus
20	chr13:111274600-111284200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:111274600-111284200	Strong transcription	Adipose Nuclei	Adipose
22	chr13:111274600-111284200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr13:111274600-111284400	Strong transcription	Placenta	Placenta
24	chr13:111274600-111284400	Strong transcription	Dnd41	blood
25	chr13:111274600-111285000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr13:111274800-111280200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:111274800-111284000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr13:111274800-111284200	Strong transcription	Primary T cells from cord blood	blood
29	chr13:111274800-111284400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr13:111274800-111284400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr13:111275000-111281600	Strong transcription	Fetal Brain Female	brain
32	chr13:111275600-111287400	Weak transcription	K562	blood
33	chr13:111275800-111280600	Weak transcription	NHDF-Ad	bronchial
34	chr13:111275800-111281800	Weak transcription	HSMMtube	muscle
35	chr13:111276000-111280200	Weak transcription	Psoas Muscle	Psoas
36	chr13:111276000-111280800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr13:111276000-111286000	Weak transcription	HUVEC	blood vessel
38	chr13:111276000-111286200	Weak transcription	A549	lung
39	chr13:111276200-111281000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:111277000-111281400	Strong transcription	Brain Germinal Matrix	brain
41	chr13:111277000-111282400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:111277000-111284200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:111277200-111281400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:111277400-111280800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:111277600-111281800	Weak transcription	Primary B cells from cord blood	blood
46	chr13:111277800-111281200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr13:111277800-111283000	Weak transcription	Hela-S3	cervix
48	chr13:111277800-111284400	Strong transcription	Fetal Muscle Leg	muscle
49	chr13:111277800-111286800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr13:111278000-111286600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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