Variant report

Variant	rs1030830
Chromosome Location	chr4:130025117-130025118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:130006908..130009786-chr4:130024045..130026428,2	K562	blood:
2	chr4:130016002..130020689-chr4:130022146..130025505,4	K562	blood:

Variant related genes	Relation type
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494317	0.89[JPT][hapmap]
rs10518539	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs12500341	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12500557	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs12503465	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12504200	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12512345	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1376202	0.93[YRI][hapmap]
rs17185550	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs17349255	0.90[JPT][hapmap]
rs17416188	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17416706	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1877836	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs1900397	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2044523	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2597837	0.93[YRI][hapmap]
rs2655311	0.84[YRI][hapmap]
rs280601	0.93[YRI][hapmap]
rs36195612	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3980331	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4423892	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs4975191	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4975293	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975294	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4975302	0.84[AFR][1000 genomes]
rs55925207	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59540486	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6825433	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs6830023	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6832138	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs6835359	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs6840353	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs6845314	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6847784	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72683669	0.90[EUR][1000 genomes]
rs72683673	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72683684	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72683693	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72685321	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685324	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72685328	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72685351	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72685352	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72685353	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72685365	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7675408	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs921375	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs921376	0.85[ASN][1000 genomes]
rs921377	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1030830	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130031400	Weak transcription	Pancreas	Pancrea
2	chr4:130017600-130031400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:130017600-130040400	Weak transcription	Lung	lung
4	chr4:130017800-130026400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:130017800-130027200	Weak transcription	Small Intestine	intestine
6	chr4:130017800-130030800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:130017800-130031400	Weak transcription	Aorta	Aorta
8	chr4:130017800-130031400	Weak transcription	Left Ventricle	heart
9	chr4:130017800-130031400	Weak transcription	Ovary	ovary
10	chr4:130017800-130031400	Weak transcription	Right Ventricle	heart
11	chr4:130017800-130031600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:130017800-130032600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:130017800-130032800	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:130017800-130033400	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:130017800-130033400	Weak transcription	Thymus	Thymus
16	chr4:130017800-130034200	Weak transcription	Colonic Mucosa	Colon
17	chr4:130018000-130025400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:130018000-130026400	Weak transcription	Fetal Kidney	kidney
19	chr4:130018000-130028000	Weak transcription	NH-A	brain
20	chr4:130018000-130030200	Weak transcription	Primary T cells from cord blood	blood
21	chr4:130018000-130030400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:130018000-130030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:130018000-130031000	Weak transcription	Fetal Thymus	thymus
24	chr4:130018000-130031400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:130018000-130031400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:130018000-130031400	Weak transcription	Fetal Stomach	stomach
27	chr4:130018000-130032400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:130018000-130033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:130018000-130033200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:130018000-130033400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:130018000-130034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:130018200-130030600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:130018200-130031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:130018200-130032400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:130018600-130025200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:130018600-130025600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:130018600-130032000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:130018800-130033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:130020200-130030400	Weak transcription	K562	blood
41	chr4:130020600-130030200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:130023600-130026800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr4:130023600-130033400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr4:130023800-130026400	Strong transcription	Liver	Liver
45	chr4:130024200-130025800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:130024200-130030600	Weak transcription	Fetal Heart	heart
47	chr4:130024400-130026000	Strong transcription	Primary B cells from cord blood	blood
48	chr4:130024400-130026000	Strong transcription	Dnd41	blood
49	chr4:130024400-130026400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:130024400-130026400	Strong transcription	Rectal Mucosa Donor 29	rectum

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