Variant report

Variant	rs6825433
Chromosome Location	chr4:129841515-129841516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1030830	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs10518539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500341	0.88[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12503465	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs12504200	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs12512345	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17349255	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17416188	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs17416706	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs1900397	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1993035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044523	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2122589	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4423892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975191	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4975286	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975294	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6814450	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815768	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6832138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6840353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847784	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs72683636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683654	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs921375	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs921376	0.81[AMR][1000 genomes]
rs921377	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv533785	chr4:129785683-129857992	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a
20	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
21	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
22	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
23	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6825433	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129793800-129907200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:129794400-129860200	Weak transcription	Thymus	Thymus
3	chr4:129810400-129847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:129810400-129847400	Weak transcription	Fetal Intestine Large	intestine
5	chr4:129810600-129847200	Weak transcription	Dnd41	blood
6	chr4:129821400-129867800	Weak transcription	Fetal Intestine Small	intestine
7	chr4:129829200-129849600	Weak transcription	Pancreas	Pancrea
8	chr4:129829800-129873000	Weak transcription	Brain Substantia Nigra	brain
9	chr4:129833800-129848400	Weak transcription	Fetal Stomach	stomach
10	chr4:129834400-129862800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:129834800-129907400	Weak transcription	Aorta	Aorta
12	chr4:129835000-129847400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:129836600-129846000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:129837000-129848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:129837200-129859600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:129837600-129850600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:129837600-129888200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:129838400-129850000	Weak transcription	Lung	lung
19	chr4:129839200-129846000	Weak transcription	Fetal Thymus	thymus
20	chr4:129839400-129847200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:129839400-129860200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:129839400-129862800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:129839600-129846200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:129839600-129854200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:129839600-129856400	Weak transcription	Primary B cells from cord blood	blood
26	chr4:129839600-129882800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:129839800-129846000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:129839800-129847200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:129839800-129847400	Weak transcription	Primary T cells from cord blood	blood
30	chr4:129839800-129862200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:129839800-129882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:129839800-129907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:129840000-129845800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:129840000-129848600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:129840600-129863400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:129841000-129907400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:129841200-129841800	ZNF genes & repeats	Psoas Muscle	Psoas

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