Variant report

Variant	rs729438
Chromosome Location	chr14:104092789-104092790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr14:104092777-104093091	HepG2	liver:	n/a	n/a
2	NFIC	chr14:104092575-104092868	GM12878	blood:	n/a	n/a
3	RUNX3	chr14:104092484-104092910	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:104092636-104093638	HepG2	liver:	n/a	n/a
5	RUNX3	chr14:104092511-104092869	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:104092649..104097026-chr14:104179930..104185119,7	MCF-7	breast:
2	chr14:104092617..104095465-chr14:104143281..104145342,2	MCF-7	breast:
3	chr14:104026823..104028811-chr14:104092754..104094269,2	K562	blood:
4	chr14:104087141..104088992-chr14:104091029..104093506,2	MCF-7	breast:
5	chr14:104026845..104031617-chr14:104090112..104098528,12	MCF-7	breast:
6	chr14:104091966..104093506-chr14:104127294..104130237,2	MCF-7	breast:
7	chr14:104091773..104098220-chr14:104179036..104183968,10	MCF-7	breast:
8	chr14:104089914..104092902-chr14:104103042..104105826,2	K562	blood:
9	chr14:104092569..104093219-chr14:104159447..104160094,2	MCF-7	breast:
10	chr14:104089889..104092847-chr14:104093725..104096816,6	K562	blood:
11	chr14:104086723..104088559-chr14:104090866..104093232,2	K562	blood:
12	chr14:104026767..104030601-chr14:104092111..104097061,5	MCF-7	breast:
13	chr14:104091792..104094435-chr14:104270981..104273053,2	MCF-7	breast:
14	chr14:104088488..104094508-chr14:104095620..104100899,7	K562	blood:

No data

Variant related genes	Relation type
KLC1	TF binding region
ENSG00000126215	Chromatin interaction
ENSG00000166170	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000269963	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000256053	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10459574	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11540512	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11844466	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11846404	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11846838	0.81[AFR][1000 genomes]
rs11851000	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11851616	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12147645	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12590968	0.87[AFR][1000 genomes]
rs12884809	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12887734	0.80[AMR][1000 genomes]
rs12888993	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12889403	0.80[CHD][hapmap]
rs12889731	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12892038	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12896171	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1606	0.83[AFR][1000 genomes]
rs1799796	0.83[AFR][1000 genomes]
rs2273175	0.90[JPT][hapmap]
rs2296482	0.80[CHD][hapmap]
rs2403197	0.86[ASW][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2896487	0.81[AMR][1000 genomes]
rs3212038	0.81[AFR][1000 genomes]
rs3212076	0.83[AFR][1000 genomes]
rs3212090	0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs34000399	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34026011	0.80[CHD][hapmap];0.81[AMR][1000 genomes]
rs34843146	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35011804	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35229468	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35921969	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4525427	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4900590	0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4900591	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4906335	0.82[CHD][hapmap]
rs4906338	0.83[AMR][1000 genomes]
rs4906347	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4906350	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906356	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57072546	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60249782	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61637848	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs67899457	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71417868	0.80[AMR][1000 genomes]
rs71417869	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7148456	0.80[CHD][hapmap]
rs7148857	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8017993	0.80[CHD][hapmap];0.82[AMR][1000 genomes]
rs8021229	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
9	esv3490243	chr14:104083248-104099394	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
10	esv3490244	chr14:104083248-104099394	Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
11	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs729438	KLC1	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104089600-104092800	Enhancers	Spleen	Spleen
2	chr14:104089800-104093600	Enhancers	Lung	lung
3	chr14:104090000-104093000	Enhancers	HSMMtube	muscle
4	chr14:104090200-104092800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:104090200-104092800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr14:104090200-104092800	Enhancers	Duodenum Mucosa	Duodenum
7	chr14:104090200-104092800	Enhancers	Esophagus	oesophagus
8	chr14:104090200-104092800	Enhancers	HSMM	muscle
9	chr14:104090200-104093000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:104090200-104093400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:104090200-104093400	Enhancers	Fetal Muscle Leg	muscle
12	chr14:104090200-104094400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:104090200-104094600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:104090200-104094600	Enhancers	Placenta	Placenta
15	chr14:104090400-104092800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr14:104090400-104092800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr14:104090400-104093400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:104090400-104094200	Weak transcription	Liver	Liver
19	chr14:104090400-104094400	Weak transcription	Aorta	Aorta
20	chr14:104090600-104093000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:104090600-104093000	Enhancers	Thymus	Thymus
22	chr14:104090600-104093400	Enhancers	Fetal Thymus	thymus
23	chr14:104090600-104094000	Weak transcription	Colon Smooth Muscle	Colon
24	chr14:104090800-104094000	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:104090800-104094200	Weak transcription	Fetal Lung	lung
26	chr14:104091000-104094600	Weak transcription	Gastric	stomach
27	chr14:104091400-104092800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr14:104091400-104094000	Weak transcription	K562	blood
29	chr14:104091400-104094200	Weak transcription	Fetal Heart	heart
30	chr14:104091400-104094400	Weak transcription	Pancreas	Pancrea
31	chr14:104091600-104093000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr14:104091600-104094000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr14:104091600-104094000	Weak transcription	Right Ventricle	heart
34	chr14:104091600-104094200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:104091600-104094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr14:104091600-104094400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:104091600-104094400	Enhancers	Fetal Muscle Trunk	muscle
38	chr14:104091600-104094400	Weak transcription	Psoas Muscle	Psoas
39	chr14:104091800-104092800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:104091800-104093000	Enhancers	Primary B cells from peripheral blood	blood
41	chr14:104091800-104093000	Enhancers	A549	lung
42	chr14:104091800-104094000	Weak transcription	Stomach Mucosa	stomach
43	chr14:104091800-104094200	Weak transcription	Right Atrium	heart
44	chr14:104091800-104094400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr14:104092000-104092800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr14:104092000-104092800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr14:104092000-104092800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr14:104092000-104092800	Enhancers	Dnd41	blood
49	chr14:104092000-104093000	Enhancers	GM12878-XiMat	blood
50	chr14:104092000-104093200	Enhancers	Primary B cells from cord blood	blood

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