Variant report

Variant	rs3846298
Chromosome Location	chr4:175429213-175429214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175428257..175430078-chr4:175431742..175433720,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11133042	0.93[GIH][hapmap]
rs1816204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2555660	0.80[ASN][1000 genomes]
rs2612656	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2612694	0.86[ASN][1000 genomes]
rs3857075	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6419992	0.90[ASN][1000 genomes]
rs6835564	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7685956	1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7691993	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525487	chr4:175400104-175470867	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv880289	chr4:175412975-175437117	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3846298	HMGB2	cis	cerebellum	SCAN
rs3846298	HAND2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175396000-175442800	Weak transcription	Esophagus	oesophagus
2	chr4:175410000-175440800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:175410800-175430800	Weak transcription	Gastric	stomach
4	chr4:175410800-175440000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:175418000-175438600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:175418600-175437800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:175418800-175435600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:175419200-175438600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:175419400-175431000	Weak transcription	Colonic Mucosa	Colon
10	chr4:175420600-175441000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:175421000-175439200	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:175424000-175429600	Strong transcription	Placenta	Placenta
13	chr4:175425200-175431800	Weak transcription	Fetal Intestine Small	intestine
14	chr4:175425800-175429400	Strong transcription	Fetal Intestine Large	intestine
15	chr4:175426000-175431600	Weak transcription	Fetal Stomach	stomach
16	chr4:175427400-175433600	Weak transcription	A549	lung
17	chr4:175427400-175434200	Weak transcription	Small Intestine	intestine
18	chr4:175427400-175438400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:175427400-175440600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:175427400-175443000	Weak transcription	Lung	lung
21	chr4:175427600-175433000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:175427600-175441800	Weak transcription	Fetal Thymus	thymus
23	chr4:175427800-175435800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:175428000-175439400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:175428600-175429400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:175428800-175429400	Strong transcription	Primary T cells from cord blood	blood
27	chr4:175428800-175429400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr4:175428800-175432400	Strong transcription	Liver	Liver
29	chr4:175429200-175436200	Weak transcription	Stomach Mucosa	stomach

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