Variant report

Variant	rs12500341
Chromosome Location	chr4:129868282-129868283
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1030830	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]
rs10518539	0.88[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs12500557	0.85[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs12503465	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504200	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512345	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17185550	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs17349255	0.80[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs17416188	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17416706	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1900397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1993035	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs2044523	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36195612	0.87[ASN][1000 genomes]
rs3980331	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4423892	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs4975191	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975286	0.80[ASN][1000 genomes]
rs4975293	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55925207	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59540486	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6825433	0.88[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs6830023	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6832138	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6835359	0.84[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs6840353	0.88[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs6845314	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847784	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72683669	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72683673	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683684	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683693	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72685321	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72685324	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685328	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685351	0.91[ASN][1000 genomes]
rs72685352	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72685353	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72685365	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7675408	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921375	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs921376	0.97[ASN][1000 genomes]
rs921377	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv461637	chr4:129774375-129924977	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595397	chr4:129774375-129924977	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv1034996	chr4:129777825-129905255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv537249	chr4:129777825-129905255	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv1022446	chr4:129778025-129905116	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv537250	chr4:129778025-129905116	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv1030296	chr4:129778025-129920680	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv537251	chr4:129778025-129920680	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	esv2830419	chr4:129785483-129905256	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
19	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
20	nsv1026722	chr4:129801602-129929219	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv537252	chr4:129801602-129929219	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv595399	chr4:129835649-129924852	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1020327	chr4:129859624-129914665	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12500341	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs12500341	SLC8A3	trans	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129793800-129907200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:129829800-129873000	Weak transcription	Brain Substantia Nigra	brain
3	chr4:129834800-129907400	Weak transcription	Aorta	Aorta
4	chr4:129837600-129888200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:129839600-129882800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:129839800-129882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:129839800-129907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:129841000-129907400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:129843600-129888000	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:129845000-129882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:129845400-129907400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:129845800-129907200	Weak transcription	Ovary	ovary
13	chr4:129847800-129895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:129850600-129869600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:129851000-129879000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:129854600-129870000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:129855200-129907800	Weak transcription	K562	blood
18	chr4:129855400-129871400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:129855400-129895200	Weak transcription	Fetal Kidney	kidney
20	chr4:129856400-129907200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:129858600-129891200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:129858800-129870600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:129859600-129868600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:129861000-129907200	Weak transcription	Thymus	Thymus
25	chr4:129862000-129868600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:129862000-129869600	Weak transcription	Fetal Heart	heart
27	chr4:129862200-129870000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:129862200-129877600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:129862400-129881600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:129862400-129924200	Weak transcription	Colonic Mucosa	Colon
31	chr4:129862800-129868800	Strong transcription	Fetal Thymus	thymus
32	chr4:129863000-129868600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:129863400-129882800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:129863600-129892000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:129863800-129871200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:129863800-129888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:129864000-129871200	Weak transcription	NHDF-Ad	bronchial
38	chr4:129864000-129871400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:129864000-129874200	Weak transcription	Psoas Muscle	Psoas
40	chr4:129864000-129875000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:129864000-129882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:129864000-129882800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:129864000-129895400	Weak transcription	NHLF	lung
44	chr4:129864000-129918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:129864200-129869800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:129864200-129870200	Weak transcription	Spleen	Spleen
47	chr4:129864200-129895400	Weak transcription	Fetal Lung	lung
48	chr4:129864400-129874000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:129864400-129879200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:129864400-129882600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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