Variant report

Variant	rs6413428
Chromosome Location	chr5:42800724-42800725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42800716..42803612-chr5:42804755..42806774,2	K562	blood:

Variant related genes	Relation type
ENSG00000272234	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10038285	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10038477	0.90[CEU][hapmap]
rs10038990	1.00[ASN][1000 genomes]
rs10041108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10041130	1.00[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs10044169	0.90[CEU][hapmap]
rs10045847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10045863	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10050889	0.90[CEU][hapmap]
rs10056315	1.00[ASN][1000 genomes]
rs10061833	0.90[CEU][hapmap]
rs10067153	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10070118	1.00[ASN][1000 genomes]
rs10070249	1.00[ASN][1000 genomes]
rs10072083	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10072749	1.00[ASN][1000 genomes]
rs10077296	0.90[CEU][hapmap]
rs10440649	1.00[CHB][hapmap]
rs10473288	0.81[EUR][1000 genomes]
rs10805665	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs10941583	1.00[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10941588	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10941590	0.80[YRI][hapmap]
rs1105983	1.00[ASN][1000 genomes]
rs1109882	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11951328	1.00[ASN][1000 genomes]
rs11957404	1.00[CHB][hapmap]
rs12514437	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12518067	0.90[CEU][hapmap]
rs13153784	0.84[YRI][hapmap]
rs13154178	0.81[YRI][hapmap]
rs13168440	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13171505	1.00[ASN][1000 genomes]
rs13172646	1.00[ASN][1000 genomes]
rs13174226	1.00[CHB][hapmap]
rs13182117	1.00[CHB][hapmap]
rs13184699	0.80[AFR][1000 genomes]
rs13187223	1.00[ASN][1000 genomes]
rs13189374	1.00[ASN][1000 genomes]
rs13354167	1.00[CHB][hapmap]
rs1423655	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes]
rs2081164	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230808	0.96[EUR][1000 genomes]
rs230811	0.96[EUR][1000 genomes]
rs28705009	1.00[ASN][1000 genomes]
rs28919899	1.00[ASN][1000 genomes]
rs28919913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910854	0.95[EUR][1000 genomes]
rs2910860	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes]
rs2910863	0.95[EUR][1000 genomes]
rs2910866	0.95[EUR][1000 genomes]
rs2910878	0.89[CEU][hapmap]
rs2972780	0.85[CEU][hapmap]
rs2973008	0.95[EUR][1000 genomes]
rs34086275	1.00[ASN][1000 genomes]
rs34159518	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34829612	1.00[ASN][1000 genomes]
rs34831882	1.00[ASN][1000 genomes]
rs35904649	1.00[ASN][1000 genomes]
rs3877899	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242116	0.90[CEU][hapmap]
rs4242117	0.90[CEU][hapmap]
rs4242119	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs4242122	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4242123	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4242124	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4273617	0.90[CEU][hapmap]
rs4283796	1.00[ASN][1000 genomes]
rs4292454	1.00[CHB][hapmap]
rs4357043	0.85[CEU][hapmap]
rs4376276	0.86[EUR][1000 genomes]
rs4394131	0.85[CEU][hapmap]
rs4569879	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4590183	0.85[CEU][hapmap]
rs4637559	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4866793	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4866948	0.90[CEU][hapmap]
rs4866955	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4866956	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4866957	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5025611	1.00[CHB][hapmap]
rs6179	0.85[CEU][hapmap]
rs6414898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6451627	0.85[CEU][hapmap]
rs6451634	1.00[CHB][hapmap]
rs6451641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6451643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863953	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6871947	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6873340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6873545	0.85[CEU][hapmap]
rs6886047	0.85[CEU][hapmap]
rs6896899	1.00[ASN][1000 genomes]
rs71627561	1.00[ASN][1000 genomes]
rs7442754	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7444761	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7701605	0.90[CEU][hapmap]
rs7702524	1.00[CHB][hapmap]
rs7703289	0.81[YRI][hapmap]
rs7709790	1.00[CHB][hapmap]
rs7710105	1.00[ASN][1000 genomes]
rs7715032	0.81[CEU][hapmap]
rs7722920	1.00[ASN][1000 genomes]
rs9292854	1.00[CHB][hapmap]
rs9292859	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription 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 lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6413428	CARD6	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42778000-42800800	Weak transcription	Ovary	ovary
2	chr5:42788600-42807600	Weak transcription	Primary T cells from cord blood	blood
3	chr5:42789400-42800800	Weak transcription	Gastric	stomach
4	chr5:42789600-42800800	Weak transcription	Pancreas	Pancrea
5	chr5:42789600-42813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:42790800-42802200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:42791400-42811200	Weak transcription	Fetal Thymus	thymus
8	chr5:42792000-42807600	Weak transcription	NHDF-Ad	bronchial
9	chr5:42794400-42802800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:42794600-42800800	Weak transcription	Aorta	Aorta
11	chr5:42795600-42810200	Weak transcription	Thymus	Thymus
12	chr5:42795800-42800800	Weak transcription	Fetal Stomach	stomach
13	chr5:42795800-42801000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:42797000-42810600	Weak transcription	Esophagus	oesophagus
15	chr5:42797400-42802800	Weak transcription	GM12878-XiMat	blood
16	chr5:42797400-42810800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:42797600-42800800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:42797600-42800800	Weak transcription	Brain Germinal Matrix	brain
19	chr5:42797600-42800800	Weak transcription	Fetal Kidney	kidney
20	chr5:42797600-42808200	Weak transcription	HSMM	muscle
21	chr5:42797800-42800800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:42797800-42809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:42798000-42800800	Weak transcription	Psoas Muscle	Psoas
24	chr5:42798200-42800800	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:42798200-42800800	Weak transcription	Left Ventricle	heart
26	chr5:42798200-42808400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:42798200-42811200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:42798400-42800800	Weak transcription	Fetal Intestine Small	intestine
29	chr5:42798400-42801000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:42798600-42800800	Weak transcription	Lung	lung
31	chr5:42798600-42806200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:42798600-42808200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:42798800-42801000	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:42798800-42806200	Weak transcription	Brain Angular Gyrus	brain
35	chr5:42798800-42806400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:42799000-42800800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:42799000-42800800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:42799000-42800800	Weak transcription	Spleen	Spleen
39	chr5:42799000-42800800	Weak transcription	HepG2	liver
40	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
41	chr5:42799200-42800800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:42799200-42800800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:42799200-42800800	Weak transcription	Fetal Intestine Large	intestine
44	chr5:42799200-42800800	Weak transcription	Right Ventricle	heart
45	chr5:42799400-42801600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:42799400-42807000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:42799400-42807400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:42799400-42808200	Weak transcription	Colonic Mucosa	Colon
49	chr5:42799600-42801200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:42799600-42807600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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