Variant report

Variant	rs2120060
Chromosome Location	chr13:76412900-76412901
allele	A/G
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	NRF1	chr13:76412750-76412914	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr13:76412847-76413142	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12427729	0.83[CEU][hapmap];0.81[CHD][hapmap];0.82[AMR][1000 genomes]
rs12428617	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12428746	0.84[CHB][hapmap]
rs12430940	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17065074	0.82[ASN][1000 genomes]
rs17065145	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.86[MKK][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120061	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.92[MKK][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2165774	0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs2241913	0.82[ASN][1000 genomes]
rs2296093	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736858	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759445	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.92[MKK][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3783025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825439	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41287008	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4885357	0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs61959583	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9318380	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9530471	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9544047	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9544049	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9544050	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9544051	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9544053	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9544056	0.92[CHB][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9544059	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[AMR][1000 genomes]

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:100 , 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	chr13:76403600-76414400	Weak transcription	Right Ventricle	heart
47	chr13:76403600-76416200	Weak transcription	Fetal Heart	heart
48	chr13:76404200-76414400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr13:76404800-76415000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr13:76404800-76418400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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