Variant report

Variant	rs12478238
Chromosome Location	chr2:128326370-128326371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128283723..128286388-chr2:128321696..128326699,5	MCF-7	breast:
2	chr2:128318000..128319961-chr2:128323554..128326504,2	K562	blood:

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10803588	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10928772	0.84[EUR][1000 genomes]
rs10928773	0.84[EUR][1000 genomes]
rs12477670	0.86[EUR][1000 genomes]
rs12616515	0.84[EUR][1000 genomes]
rs13025351	0.84[EUR][1000 genomes]
rs13407823	0.84[EUR][1000 genomes]
rs35136538	0.84[EUR][1000 genomes]
rs35583378	0.84[EUR][1000 genomes]
rs35971939	0.84[EUR][1000 genomes]
rs4662739	0.82[EUR][1000 genomes]
rs4662740	0.84[EUR][1000 genomes]
rs62156607	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv998519	chr2:128292190-128352032	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008180	chr2:128295320-128355891	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1005109	chr2:128295320-128363255	Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1001939	chr2:128295320-128363608	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1015051	chr2:128295320-128372079	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1011937	chr2:128295320-128405921	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1008294	chr2:128295320-128420654	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1007207	chr2:128295320-128429775	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1003004	chr2:128295320-128474326	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv1013998	chr2:128299079-128355891	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1005799	chr2:128299079-128363255	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1013925	chr2:128299079-128363648	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1001780	chr2:128299079-128364126	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv999302	chr2:128299079-128372079	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1008457	chr2:128299079-128405921	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv1009514	chr2:128299079-128420654	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv1006421	chr2:128299079-128473079	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
19	nsv1004877	chr2:128299079-128479640	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
20	nsv875015	chr2:128305196-128495645	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
21	nsv1012655	chr2:128306660-128352032	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv1001624	chr2:128306660-128420654	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128317800-128334200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:128321000-128329000	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr2:128321000-128329000	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:128321200-128328600	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr2:128321600-128329200	Strong transcription	Fetal Intestine Large	intestine
6	chr2:128321600-128352200	Strong transcription	Fetal Intestine Small	intestine
7	chr2:128321800-128330000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:128322000-128329600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr2:128323400-128328400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:128323800-128334000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:128324600-128331000	Weak transcription	Colonic Mucosa	Colon
12	chr2:128324600-128333600	Weak transcription	Spleen	Spleen
13	chr2:128324800-128326800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:128324800-128327000	Weak transcription	Left Ventricle	heart
15	chr2:128325000-128328400	Enhancers	Placenta	Placenta
16	chr2:128325200-128328000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr2:128325400-128329000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:128325600-128326800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:128325600-128326800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:128325600-128327600	Enhancers	Psoas Muscle	Psoas
21	chr2:128325600-128333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:128325800-128326800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:128325800-128327000	Enhancers	Osteobl	bone
24	chr2:128325800-128328200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:128325800-128328800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:128326000-128327000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:128326000-128327000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:128326000-128327000	Weak transcription	Right Atrium	heart
29	chr2:128326000-128328800	Enhancers	Adipose Nuclei	Adipose
30	chr2:128326200-128327000	Weak transcription	Right Ventricle	heart
31	chr2:128326200-128327400	Enhancers	Cortex derived primary cultured neurospheres	brain

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