Variant report

Variant	rs4900590
Chromosome Location	chr14:104146421-104146422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr14:104146288-104146575	GM12878	blood:	n/a	n/a
2	POLR2A	chr14:104144700-104146457	K562	blood:	n/a	n/a
3	CTCF	chr14:104145569-104146448	A549	lung:	n/a	chr14:104145917-104145935 chr14:104145918-104145934 chr14:104145919-104145932
4	POLR2A	chr14:104146253-104146478	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:104140406..104143075-chr14:104144410..104146768,3	MCF-7	breast:
2	chr14:104027610..104029440-chr14:104145265..104147418,2	MCF-7	breast:
3	chr14:104094737..104096335-chr14:104145973..104147742,2	K562	blood:
4	chr14:104041686..104043477-chr14:104144535..104146675,2	MCF-7	breast:
5	chr14:104141653..104144496-chr14:104146001..104148287,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XRCC3-1	chr14:104146166-104147812	ENSG00000246451
2	lnc-XRCC3-1	chr14:104146166-104147812	NONHSAT040191

No data

Variant related genes	Relation type
KLC1	TF binding region
ENSG00000256053	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000264904	Chromatin interaction
ENSG00000166170	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10459574	0.84[ASN][1000 genomes]
rs11540512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11844466	0.87[AFR][1000 genomes]
rs11846404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11846838	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11851000	0.85[AFR][1000 genomes]
rs11851616	0.87[AFR][1000 genomes]
rs12147645	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12884809	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12888993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12889403	0.84[JPT][hapmap]
rs12889731	0.86[ASN][1000 genomes]
rs12892038	0.87[AFR][1000 genomes]
rs12896171	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1606	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1799796	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273175	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295152	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296482	0.80[JPT][hapmap]
rs2403197	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3212024	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3212038	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3212076	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212090	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34000399	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34843146	0.87[AFR][1000 genomes]
rs35011804	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35921969	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4525427	0.87[AFR][1000 genomes]
rs4900591	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4900592	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906335	0.80[JPT][hapmap]
rs4906350	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4906356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57072546	0.83[AFR][1000 genomes]
rs60249782	0.83[AFR][1000 genomes]
rs61637848	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7140568	0.81[JPT][hapmap]
rs7148456	0.80[JPT][hapmap]
rs7148857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729438	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]
rs8017993	0.80[JPT][hapmap]
rs8021229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
12	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv1041347	chr14:104141217-104186372	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking 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	36 gene(s)	inside rSNPs	diseases
14	nsv902309	chr14:104143385-104198251	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv902310	chr14:104143385-104205811	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4900590	KLC1	Cis_1M	lymphoblastoid	RTeQTL
rs4900590	RP11-73M18.8	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:104117800-104157000	Strong transcription	Dnd41	blood
3	chr14:104117800-104176000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr14:104118800-104175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:104119200-104155600	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr14:104119200-104173000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:104119400-104147800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr14:104119400-104157000	Strong transcription	Fetal Thymus	thymus
9	chr14:104119400-104161800	Strong transcription	Fetal Intestine Small	intestine
10	chr14:104119400-104164600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr14:104119400-104175200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr14:104120000-104177000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr14:104120200-104149800	Strong transcription	Fetal Muscle Leg	muscle
14	chr14:104120200-104155000	Strong transcription	Fetal Brain Female	brain
15	chr14:104120200-104161400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr14:104120200-104161800	Strong transcription	Fetal Intestine Large	intestine
17	chr14:104120400-104150000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr14:104120400-104157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:104120400-104157000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr14:104120400-104161200	Strong transcription	Fetal Stomach	stomach
21	chr14:104120600-104155000	Strong transcription	Brain Germinal Matrix	brain
22	chr14:104120800-104157200	Strong transcription	Thymus	Thymus
23	chr14:104121000-104154200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr14:104121000-104154800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:104121000-104162000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:104122800-104153000	Strong transcription	Liver	Liver
27	chr14:104123400-104155200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:104124600-104147800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr14:104124600-104169800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr14:104124600-104169800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr14:104125200-104155400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr14:104130400-104147800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:104130400-104153000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:104130600-104149800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:104130600-104150400	Strong transcription	Adipose Nuclei	Adipose
36	chr14:104130600-104159600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr14:104130800-104155600	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr14:104131000-104161800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr14:104131400-104155200	Strong transcription	Brain Anterior Caudate	brain
40	chr14:104132000-104155000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr14:104132200-104154800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:104132800-104156000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:104133400-104177200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr14:104133800-104147800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr14:104133800-104150400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr14:104133800-104153600	Strong transcription	Osteobl	bone
47	chr14:104133800-104154800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr14:104133800-104157000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr14:104134000-104147800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr14:104134000-104152400	Strong transcription	H9 Cell Line	embryonic stem cell

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