Variant report

Variant	rs4975293
Chromosome Location	chr4:129909429-129909430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129900386..129903021-chr4:129908411..129910284,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1030830	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12500341	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503465	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12504200	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512345	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17416188	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17416706	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1900397	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044523	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36195612	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3980331	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975191	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975294	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55925207	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59540486	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830023	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6845314	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6847784	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72683669	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72683673	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72683684	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72683693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685321	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72685324	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72685328	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72685351	0.92[ASN][1000 genomes]
rs72685352	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685353	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685365	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7675408	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921375	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921376	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921377	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4975293	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129862400-129924200	Weak transcription	Colonic Mucosa	Colon
2	chr4:129864000-129918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:129866600-129916600	Weak transcription	Right Ventricle	heart
4	chr4:129866800-129916200	Weak transcription	Hela-S3	cervix
5	chr4:129868200-129935600	Weak transcription	HSMM	muscle
6	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
7	chr4:129883200-129923400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:129883400-129912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:129887000-129918800	Weak transcription	Psoas Muscle	Psoas
10	chr4:129887800-129918000	Weak transcription	Fetal Heart	heart
11	chr4:129895600-129916800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:129895800-129910400	Weak transcription	NHLF	lung
13	chr4:129901200-129918000	Weak transcription	HUVEC	blood vessel
14	chr4:129901800-129918600	Weak transcription	NHDF-Ad	bronchial
15	chr4:129901800-129920600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:129901800-129921200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:129902000-129911600	Weak transcription	Osteobl	bone
18	chr4:129902400-129912600	Weak transcription	HMEC	breast
19	chr4:129902400-129922400	Weak transcription	NH-A	brain
20	chr4:129903000-129910000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:129903200-129920600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:129904600-129909800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:129905000-129917800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:129906200-129935800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:129906400-129917400	Weak transcription	Stomach Mucosa	stomach
26	chr4:129906600-129912400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:129907600-129911200	Weak transcription	Brain Anterior Caudate	brain
28	chr4:129907600-129920600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:129907800-129909800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:129908200-129909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:129908200-129910000	Weak transcription	Fetal Lung	lung
32	chr4:129908200-129912200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:129908200-129916600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:129908200-129916600	Weak transcription	Fetal Intestine Small	intestine
35	chr4:129908200-129916800	Weak transcription	Aorta	Aorta
36	chr4:129908200-129916800	Weak transcription	Esophagus	oesophagus
37	chr4:129908200-129916800	Weak transcription	Fetal Stomach	stomach
38	chr4:129908200-129916800	Weak transcription	Lung	lung
39	chr4:129908200-129916800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:129908200-129917000	Weak transcription	Ovary	ovary
41	chr4:129908200-129917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:129908200-129918000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:129908200-129918800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:129908200-129919400	Weak transcription	NHEK	skin
45	chr4:129908200-129921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:129908200-129921600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:129908200-129921800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:129908200-129927000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:129908400-129909600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:129908400-129909600	Weak transcription	Fetal Intestine Large	intestine

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