Variant report

Variant	rs3765874
Chromosome Location	chr1:210543246-210543247
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210542650..210545559-chr11:61515420..61517723,2	MCF-7	breast:
2	chr1:210542669..210544192-chr1:210705476..210708034,2	MCF-7	breast:
3	chr1:210410044..210411714-chr1:210543062..210545355,2	MCF-7	breast:
4	chr1:210542938..210544518-chr1:210591171..210592878,2	MCF-7	breast:
5	chr1:149857620..149859667-chr1:210543138..210546005,2	MCF-7	breast:
6	chr1:210417526..210420172-chr1:210543053..210546033,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184260	Chromatin interaction
ENSG00000082497	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000124915	Chromatin interaction
ENSG00000184678	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1076708	0.88[CHB][hapmap]
rs12143445	0.81[AMR][1000 genomes]
rs17016036	0.92[CHD][hapmap]
rs2143440	0.89[CEU][hapmap]
rs35655204	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765862	0.88[CEU][hapmap]
rs4844523	0.80[CHB][hapmap]
rs4845006	0.88[CHD][hapmap];0.83[JPT][hapmap]
rs4845009	0.82[AMR][1000 genomes]
rs7515805	0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551407	0.89[CEU][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap]
rs946125	0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3765874	C1orf107	cis	parietal	SCAN
rs3765874	TMEM206	cis	parietal	SCAN
rs3765874	TRAF3IP3	cis	cerebellum	SCAN
rs3765874	HHAT	cis	parietal	SCAN
rs3765874	ELK4	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
3	chr1:210532400-210545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:210534600-210546800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:210536800-210551000	Weak transcription	Right Ventricle	heart
6	chr1:210536800-210558800	Weak transcription	Fetal Stomach	stomach
7	chr1:210537000-210550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:210537800-210544600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:210538400-210547000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:210538400-210565600	Weak transcription	Esophagus	oesophagus
11	chr1:210538600-210546800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:210540800-210549600	Weak transcription	HSMMtube	muscle
13	chr1:210541000-210545000	Weak transcription	HMEC	breast
14	chr1:210541000-210545400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:210541000-210546000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:210541000-210550000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:210541200-210546800	Enhancers	HepG2	liver
18	chr1:210541400-210545600	Weak transcription	Fetal Brain Male	brain
19	chr1:210542400-210543400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:210542400-210543400	Enhancers	Fetal Brain Female	brain
21	chr1:210542600-210543400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:210542600-210543400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:210542600-210543400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
24	chr1:210542800-210543400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:210542800-210543400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:210542800-210543400	Enhancers	Fetal Heart	heart
27	chr1:210542800-210543600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr1:210542800-210543600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr1:210543000-210543400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr1:210543000-210543400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:210543000-210543400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:210543000-210543600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
33	chr1:210543200-210543400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:210543200-210543400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr1:210543200-210543400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
36	chr1:210543200-210543400	Enhancers	Brain Cingulate Gyrus	brain
37	chr1:210543200-210545400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:210543200-210546800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:210543200-210548000	Weak transcription	HSMM	muscle
40	chr1:210543200-210549800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:210543200-210555800	Weak transcription	Right Atrium	heart
42	chr1:210543200-210565200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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