Variant report

Variant	rs2273996
Chromosome Location	chr13:76410725-76410726
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	NR2F2	chr13:76410583-76410946	MCF-7	breast:	n/a	n/a
2	POLR2A	chr13:76410718-76410872	ProgFib	skin:	n/a	n/a
3	ESR1	chr13:76410617-76411003	T-47D	breast:	n/a	n/a
4	GATA3	chr13:76410603-76411132	T-47D	breast:	n/a	chr13:76410627-76410637
5	EP300	chr13:76410582-76411108	T-47D	breast:	n/a	n/a
6	GATA3	chr13:76410611-76411074	T-47D	breast:	n/a	chr13:76410627-76410637
7	FOXA1	chr13:76410642-76410979	T-47D	breast:	n/a	chr13:76410786-76410801
8	FOXA1	chr13:76410535-76411074	T-47D	breast:	n/a	chr13:76410786-76410801
9	EP300	chr13:76410646-76411041	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs4884022	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4885354	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7334674	0.86[YRI][hapmap]
rs7984837	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7986131	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7986246	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7995442	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7996791	0.82[YRI][hapmap]
rs8000656	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9318377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530473	0.84[LWK][hapmap];0.93[YRI][hapmap]
rs9593134	0.80[YRI][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2273996	LMO7	cis	parietal	SCAN
rs2273996	TBC1D4	cis	cerebellum	SCAN

Chromatin state (count:97 , 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	chr13:76387800-76415800	Weak transcription	Brain Germinal Matrix	brain
9	chr13:76387800-76427200	Weak transcription	Ovary	ovary
10	chr13:76388000-76415200	Weak transcription	Fetal Brain Female	brain
11	chr13:76388800-76415400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:76389400-76414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:76391200-76418600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:76391200-76431600	Strong transcription	Hela-S3	cervix
15	chr13:76391600-76415200	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:76392400-76415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:76393000-76416000	Weak transcription	Brain Angular Gyrus	brain
18	chr13:76393400-76415800	Weak transcription	Psoas Muscle	Psoas
19	chr13:76393600-76414400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:76393600-76416000	Weak transcription	Fetal Lung	lung
21	chr13:76394200-76415400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:76394400-76435800	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:76394800-76415800	Weak transcription	Adipose Nuclei	Adipose
24	chr13:76395600-76414400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr13:76396400-76432000	Weak transcription	Brain Substantia Nigra	brain
26	chr13:76396400-76436800	Weak transcription	Fetal Brain Male	brain
27	chr13:76396800-76415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr13:76396800-76416200	Weak transcription	Fetal Kidney	kidney
29	chr13:76398400-76415400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:76398400-76415600	Weak transcription	Brain Anterior Caudate	brain
31	chr13:76398400-76415600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr13:76398600-76414600	Weak transcription	Colonic Mucosa	Colon
33	chr13:76398600-76415200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr13:76399000-76433200	Weak transcription	Small Intestine	intestine
35	chr13:76399800-76433000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr13:76400000-76414200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:76400800-76414400	Weak transcription	Gastric	stomach
38	chr13:76400800-76414800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr13:76400800-76415800	Weak transcription	Fetal Stomach	stomach
40	chr13:76400800-76428400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr13:76401000-76414400	Weak transcription	Esophagus	oesophagus
42	chr13:76401000-76415800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:76401000-76415800	Weak transcription	Lung	lung
44	chr13:76403000-76414400	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:76403000-76414600	Weak transcription	Stomach Mucosa	stomach
46	chr13:76403400-76410800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:76403600-76414400	Weak transcription	Right Ventricle	heart
48	chr13:76403600-76416200	Weak transcription	Fetal Heart	heart
49	chr13:76404200-76414400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr13:76404800-76411400	Weak transcription	Fetal Thymus	thymus

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