Variant report

Variant	rs2238042
Chromosome Location	chr12:2271575-2271576
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	chr12:2253016..2255096-chr12:2269264..2272000,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1005618	0.86[AMR][1000 genomes]
rs1122864	0.87[AMR][1000 genomes]
rs2238034	0.88[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes]
rs2238036	0.83[JPT][hapmap]
rs2239136	0.82[CEU][hapmap]
rs2247833	0.83[JPT][hapmap]
rs2283285	0.83[CEU][hapmap]
rs4765898	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521838	chr12:2060580-2299680	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv898604	chr12:2236842-2317523	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv557053	chr12:2245636-2280942	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv468973	chr12:2245636-2285731	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1042598	chr12:2245689-2290810	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv541352	chr12:2245689-2290810	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv1840049	chr12:2245850-2272864	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1052758	chr12:2245850-2272864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv898605	chr12:2252924-2327944	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2263600-2272600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:2263800-2272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:2263800-2275000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:2264000-2272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:2265000-2272600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:2269200-2273600	Enhancers	Left Ventricle	heart
7	chr12:2269200-2273600	Enhancers	Right Ventricle	heart
8	chr12:2269200-2275000	Enhancers	Rectal Smooth Muscle	rectum
9	chr12:2269200-2275600	Enhancers	Colon Smooth Muscle	Colon
10	chr12:2269400-2275400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:2269600-2272400	Enhancers	Stomach Smooth Muscle	stomach
12	chr12:2270000-2275000	Enhancers	NHLF	lung
13	chr12:2270200-2272200	Enhancers	Aorta	Aorta
14	chr12:2270200-2272600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:2270200-2273600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:2270200-2273800	Enhancers	Fetal Heart	heart
17	chr12:2270400-2271600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:2270400-2271600	Enhancers	Lung	lung
19	chr12:2270400-2273600	Enhancers	Fetal Muscle Trunk	muscle
20	chr12:2270400-2273600	Enhancers	Right Atrium	heart
21	chr12:2270400-2273800	Enhancers	Fetal Muscle Leg	muscle
22	chr12:2270400-2274200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:2270400-2274800	Enhancers	Small Intestine	intestine
24	chr12:2270400-2275200	Enhancers	Fetal Lung	lung
25	chr12:2270600-2271600	Enhancers	Brain Cingulate Gyrus	brain
26	chr12:2270600-2271600	Enhancers	Brain Hippocampus Middle	brain
27	chr12:2270600-2271600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:2270600-2273200	Enhancers	HepG2	liver
29	chr12:2270600-2273400	Enhancers	Stomach Mucosa	stomach
30	chr12:2270600-2273400	Enhancers	Spleen	Spleen
31	chr12:2270600-2273800	Enhancers	NH-A	brain
32	chr12:2270600-2274000	Enhancers	Ovary	ovary
33	chr12:2270600-2274800	Enhancers	Adipose Nuclei	Adipose
34	chr12:2270600-2275000	Enhancers	NHDF-Ad	bronchial
35	chr12:2270600-2275800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:2270800-2271800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:2270800-2272200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:2270800-2272800	Weak transcription	Gastric	stomach
39	chr12:2270800-2273600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:2271000-2271600	Weak transcription	Fetal Thymus	thymus
41	chr12:2271000-2272000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:2271000-2272400	Enhancers	Osteobl	bone
43	chr12:2271000-2278000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:2271200-2271800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr12:2271200-2272800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr12:2271200-2274200	Enhancers	Brain Substantia Nigra	brain
47	chr12:2271400-2271600	Enhancers	Esophagus	oesophagus
48	chr12:2271400-2271600	Enhancers	Fetal Intestine Small	intestine
49	chr12:2271400-2272000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:2271400-2272400	Weak transcription	Fetal Stomach	stomach

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