Variant report

Variant	rs978730
Chromosome Location	chr1:120313254-120313255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120307608..120310232-chr1:120312392..120315286,2	MCF-7	breast:
2	chr1:120307009..120310349-chr1:120312999..120315944,3	K562	blood:
3	chr1:120312850..120316176-chr1:120320921..120324121,3	MCF-7	breast:
4	chr1:120306158..120308946-chr1:120309949..120314499,4	K562	blood:
5	chr1:120300548..120303157-chr1:120311431..120313956,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134240	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1163542	0.97[EUR][1000 genomes]
rs1163543	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1163544	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1163550	0.97[EUR][1000 genomes]
rs1177389	0.96[EUR][1000 genomes]
rs12132674	0.95[EUR][1000 genomes]
rs1814447	0.98[EUR][1000 genomes]
rs2282402	0.93[ASN][1000 genomes]
rs2582779	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582780	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582782	0.96[EUR][1000 genomes]
rs2582785	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582786	0.98[EUR][1000 genomes]
rs2582790	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843014	0.96[EUR][1000 genomes]
rs2843015	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843016	0.97[EUR][1000 genomes]
rs2843017	0.98[EUR][1000 genomes]
rs72695189	0.93[EUR][1000 genomes]
rs753425	0.99[EUR][1000 genomes]
rs930448	0.98[EUR][1000 genomes]
rs935060	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120309800-120313800	Weak transcription	Brain Anterior Caudate	brain
2	chr1:120309800-120316000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:120310000-120316200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:120310000-120316600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:120310200-120316200	Weak transcription	Psoas Muscle	Psoas
6	chr1:120310400-120315400	Weak transcription	Hela-S3	cervix
7	chr1:120310600-120314400	Enhancers	Placenta	Placenta
8	chr1:120311600-120313800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:120311600-120314000	Weak transcription	Fetal Stomach	stomach
10	chr1:120311600-120314400	Enhancers	Stomach Mucosa	stomach
11	chr1:120311600-120318800	Enhancers	Fetal Intestine Large	intestine
12	chr1:120311800-120313600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:120311800-120313600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:120311800-120313800	Weak transcription	Colonic Mucosa	Colon
15	chr1:120311800-120314000	Weak transcription	Pancreas	Pancrea
16	chr1:120311800-120315800	Enhancers	Liver	Liver
17	chr1:120311800-120315800	Weak transcription	Fetal Heart	heart
18	chr1:120311800-120316200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:120311800-120316200	Weak transcription	Left Ventricle	heart
20	chr1:120311800-120316400	Weak transcription	Adipose Nuclei	Adipose
21	chr1:120311800-120316400	Weak transcription	Ovary	ovary
22	chr1:120311800-120317800	Enhancers	HepG2	liver
23	chr1:120311800-120319600	Enhancers	Fetal Intestine Small	intestine
24	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:120311800-120325400	Weak transcription	Lung	lung
26	chr1:120312000-120313400	Weak transcription	Fetal Lung	lung
27	chr1:120312000-120313600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:120312000-120314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:120312000-120314000	Weak transcription	Fetal Kidney	kidney
30	chr1:120312000-120314200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:120312000-120314200	Weak transcription	Small Intestine	intestine
32	chr1:120312000-120314800	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:120312000-120315600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:120312000-120316400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:120312000-120316600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:120312000-120318600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:120312200-120316200	Weak transcription	Gastric	stomach
38	chr1:120312400-120315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:120312400-120316000	Weak transcription	Right Ventricle	heart
40	chr1:120312600-120316000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:120313000-120313400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:120313000-120314000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:120313200-120313800	Weak transcription	Esophagus	oesophagus
44	chr1:120313200-120314400	Enhancers	Rectal Mucosa Donor 29	rectum

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