Variant report

Variant	rs72906483
Chromosome Location	chr2:39325403-39325404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39319265..39325749-chr2:39345590..39349573,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDKL4-5	chr2:39325290-39325586	NONHSAT070221

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs41280639	0.84[ASN][1000 genomes]
rs55649188	0.89[ASN][1000 genomes]
rs57362484	1.00[ASN][1000 genomes]
rs59340802	1.00[ASN][1000 genomes]
rs61456571	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61521176	0.81[ASN][1000 genomes]
rs6735371	0.95[ASN][1000 genomes]
rs6755453	1.00[ASN][1000 genomes]
rs72906433	1.00[ASN][1000 genomes]
rs72906442	1.00[ASN][1000 genomes]
rs72906449	1.00[ASN][1000 genomes]
rs72906454	1.00[ASN][1000 genomes]
rs72906466	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906469	1.00[ASN][1000 genomes]
rs72909647	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72909674	0.83[AFR][1000 genomes]
rs72909679	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7559174	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7571797	0.95[ASN][1000 genomes]
rs7581411	0.95[ASN][1000 genomes]
rs7588123	1.00[ASN][1000 genomes]
rs7592176	1.00[ASN][1000 genomes]
rs7605889	1.00[ASN][1000 genomes]
rs7609455	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
2	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
3	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:39282600-39327400	Weak transcription	Hela-S3	cervix
6	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
8	chr2:39294600-39339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:39296400-39339400	Weak transcription	Aorta	Aorta
10	chr2:39307600-39333800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:39315200-39326800	Weak transcription	Psoas Muscle	Psoas
12	chr2:39319000-39333800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:39319600-39327800	Weak transcription	Lung	lung
14	chr2:39319600-39328200	Weak transcription	Right Atrium	heart
15	chr2:39319600-39339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:39319800-39333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:39321000-39326400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:39321000-39326800	Weak transcription	Left Ventricle	heart
20	chr2:39321000-39327600	Weak transcription	Stomach Mucosa	stomach
21	chr2:39321000-39334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:39321000-39334200	Weak transcription	Liver	Liver
23	chr2:39321000-39338600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:39321000-39344600	Weak transcription	Gastric	stomach
25	chr2:39321200-39331000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:39321200-39333800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:39321600-39326800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:39321800-39332400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:39322000-39325600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:39322400-39345200	Weak transcription	Osteobl	bone
31	chr2:39322600-39332400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:39322600-39344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:39322800-39326200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:39322800-39326600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:39322800-39326600	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:39322800-39326800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr2:39322800-39326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:39322800-39326800	Weak transcription	Thymus	Thymus
39	chr2:39322800-39327400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:39322800-39328000	Weak transcription	Primary B cells from cord blood	blood
41	chr2:39322800-39329400	Weak transcription	Spleen	Spleen
42	chr2:39322800-39333800	Weak transcription	HSMM	muscle
43	chr2:39322800-39334200	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:39322800-39334200	Weak transcription	NHLF	lung
45	chr2:39322800-39334400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:39322800-39334400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:39322800-39334400	Weak transcription	K562	blood
48	chr2:39322800-39339200	Weak transcription	Fetal Thymus	thymus
49	chr2:39322800-39345200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:39323000-39327600	Weak transcription	NHDF-Ad	bronchial

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