Variant report

Variant	rs223413
Chromosome Location	chr4:103732866-103732867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:103732039-103733588	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:103732523-103733522	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:103732859-103735361	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:103732497-103732964	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr4:103732534-103734004	K562	blood:	n/a	n/a
6	POLR2A	chr4:103732149-103733832	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103730843..103736706-chr4:103746374..103749972,8	MCF-7	breast:

Variant related genes	Relation type
UBE2D3	TF binding region
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10006474	0.83[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap]
rs10516495	0.91[CEU][hapmap];0.84[CHB][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs223317	1.00[CEU][hapmap]
rs223331	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs223361	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223366	0.83[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs223374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs223471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs223490	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2866416	0.95[CEU][hapmap]
rs4699048	0.95[CEU][hapmap];0.87[CHB][hapmap]

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	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs223413	MANBA	cis	parietal	SCAN
rs223413	MANBA	cis	cerebellum	SCAN
rs223413	KRT8P46	cis	lung	GTEx
rs223413	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs223413	CISD2	cis	cerebellum	SCAN
rs223413	MANBA	cis	multi-tissue	Pritchard
rs223413	LRRC37A15P	cis	Thyroid	GTEx
rs223413	MANBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103712400-103735000	Strong transcription	K562	blood
2	chr4:103712400-103736200	Strong transcription	Fetal Intestine Large	intestine
3	chr4:103712400-103737200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
5	chr4:103712800-103736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
8	chr4:103714800-103733200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr4:103714800-103737200	Strong transcription	Dnd41	blood
10	chr4:103716000-103736000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr4:103718200-103739200	Weak transcription	Stomach Mucosa	stomach
12	chr4:103719200-103733200	Weak transcription	Psoas Muscle	Psoas
13	chr4:103719800-103733200	Weak transcription	Small Intestine	intestine
14	chr4:103723800-103737000	Weak transcription	Colonic Mucosa	Colon
15	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:103724600-103734600	Weak transcription	Fetal Kidney	kidney
17	chr4:103725000-103740600	Weak transcription	Fetal Brain Female	brain
18	chr4:103725600-103734400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:103725800-103735800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:103726600-103733000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:103726800-103738600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:103728400-103735200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:103728400-103744400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:103728600-103737400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:103729600-103735000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr4:103729800-103734600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:103729800-103735800	Enhancers	Brain Substantia Nigra	brain
29	chr4:103730000-103734400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:103730000-103734800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr4:103730000-103740600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:103730200-103734600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:103730200-103737000	Weak transcription	Hela-S3	cervix
34	chr4:103730600-103733200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:103730600-103736000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr4:103730600-103737000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr4:103730800-103733400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:103730800-103734400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:103730800-103734600	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr4:103730800-103736000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr4:103731000-103733800	Enhancers	Ovary	ovary
42	chr4:103731000-103736600	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr4:103731200-103733200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:103731200-103733200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:103731200-103733200	Weak transcription	A549	lung
46	chr4:103731200-103733400	Weak transcription	Fetal Heart	heart
47	chr4:103731200-103733600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:103731200-103736600	Strong transcription	HSMM	muscle
49	chr4:103731200-103737000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:103731200-103737800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links