Variant report

Variant	rs12871921
Chromosome Location	chr13:76405301-76405302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr13:76404932-76405454	SK-N-SH	brain:	n/a	chr13:76405175-76405183 chr13:76405174-76405184 chr13:76405175-76405183 chr13:76405176-76405183 chr13:76405174-76405184 chr13:76405174-76405184 chr13:76405174-76405184
2	STAT3	chr13:76404983-76405306	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr13:76405300-76405458	ProgFib	skin:	n/a	n/a
4	MAFK	chr13:76405030-76405462	IMR90	lung:	n/a	chr13:76405308-76405325
5	NFIC	chr13:76404821-76405432	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr13:76405097-76405365	SK-N-SH	brain:	n/a	n/a
7	FOS	chr13:76405038-76405302	MCF10A-Er-Src	breast:	n/a	chr13:76405175-76405183 chr13:76405174-76405184 chr13:76405175-76405183 chr13:76405176-76405183 chr13:76405174-76405184 chr13:76405174-76405184 chr13:76405174-76405184

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76401876..76403467-chr13:76404663..76406392,2	K562	blood:

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10507834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12100234	1.00[CHB][hapmap]
rs12859043	0.86[ASN][1000 genomes]
rs12872230	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12877821	0.86[ASN][1000 genomes]
rs1323570	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1470273	0.86[ASN][1000 genomes]
rs17065018	1.00[CHB][hapmap]
rs17065046	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17065075	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17065126	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17065132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34083520	0.86[ASN][1000 genomes]
rs34295825	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34348643	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34713814	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34782398	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35034793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35039250	1.00[AFR][1000 genomes]
rs35353403	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35843177	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4884019	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4884020	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4885347	0.86[ASN][1000 genomes]
rs4885350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs579540	1.00[ASN][1000 genomes]
rs71434807	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71434809	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs920700	1.00[CHB][hapmap]

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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
2	chr13:76373000-76414600	Weak transcription	HMEC	breast
3	chr13:76376800-76415400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:76377600-76415800	Weak transcription	Dnd41	blood
5	chr13:76377600-76416200	Weak transcription	A549	lung
6	chr13:76378200-76415800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr13:76378400-76415600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr13:76380600-76405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:76387800-76415800	Weak transcription	Brain Germinal Matrix	brain
10	chr13:76387800-76427200	Weak transcription	Ovary	ovary
11	chr13:76388000-76415200	Weak transcription	Fetal Brain Female	brain
12	chr13:76388800-76415400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:76389400-76414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr13:76390400-76405600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:76391000-76405600	Strong transcription	Liver	Liver
16	chr13:76391200-76418600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:76391200-76431600	Strong transcription	Hela-S3	cervix
18	chr13:76391600-76415200	Weak transcription	Brain Hippocampus Middle	brain
19	chr13:76392400-76415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:76393000-76416000	Weak transcription	Brain Angular Gyrus	brain
21	chr13:76393200-76405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:76393200-76405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr13:76393400-76415800	Weak transcription	Psoas Muscle	Psoas
24	chr13:76393600-76414400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:76393600-76416000	Weak transcription	Fetal Lung	lung
26	chr13:76393800-76405600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr13:76394200-76415400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr13:76394400-76435800	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:76394800-76415800	Weak transcription	Adipose Nuclei	Adipose
30	chr13:76395600-76414400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:76396400-76432000	Weak transcription	Brain Substantia Nigra	brain
32	chr13:76396400-76436800	Weak transcription	Fetal Brain Male	brain
33	chr13:76396800-76415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:76396800-76416200	Weak transcription	Fetal Kidney	kidney
35	chr13:76397200-76405400	Strong transcription	Fetal Intestine Large	intestine
36	chr13:76398400-76415400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr13:76398400-76415600	Weak transcription	Brain Anterior Caudate	brain
38	chr13:76398400-76415600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr13:76398600-76414600	Weak transcription	Colonic Mucosa	Colon
40	chr13:76398600-76415200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:76399000-76433200	Weak transcription	Small Intestine	intestine
42	chr13:76399200-76406400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr13:76399800-76405400	Weak transcription	GM12878-XiMat	blood
44	chr13:76399800-76433000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:76400000-76414200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:76400200-76405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:76400800-76405600	Weak transcription	Pancreas	Pancrea
48	chr13:76400800-76414400	Weak transcription	Gastric	stomach
49	chr13:76400800-76414800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:76400800-76415800	Weak transcription	Fetal Stomach	stomach

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