Variant report

Variant	rs717144
Chromosome Location	chr2:86264630-86264631
allele	A/G
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	chr2:86264284-86264738	GM12878	blood:	n/a	n/a
2	TCF12	chr2:86264391-86265089	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:86264465-86264877	U87	brain:	n/a	n/a
4	MAX	chr2:86263019-86264787	NB4	blood:	n/a	n/a
5	MAX	chr2:86264394-86264854	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:86264305-86264755	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr2:86262900-86264723	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:86264478-86264681	Hela-S3	cervix:	n/a	n/a
9	RUNX3	chr2:86264346-86264894	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:86262922-86264769	GM12878	blood:	n/a	n/a
11	RCOR1	chr2:86262772-86265905	IMR90	lung:	n/a	n/a
12	PML	chr2:86264478-86264913	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:86264430-86264724	K562	blood:	n/a	n/a
14	POLR2A	chr2:86262617-86264790	GM18505	blood:	n/a	n/a
15	POLR2A	chr2:86264576-86264939	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:86264355-86264772	HUVEC	blood vessel:	n/a	n/a
17	EBF1	chr2:86262842-86264741	GM12878	blood:	n/a	n/a
18	MYC	chr2:86264571-86264757	MCF10A-Er-Src	breast:	n/a	n/a
19	TCF12	chr2:86264331-86265134	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:86264465-86264849	U87	brain:	n/a	n/a
21	CTCF	chr2:86264480-86264630	HCPEpiC	choroid plexus:	n/a	n/a
22	POLR2A	chr2:86264117-86264875	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr2:86262944-86264683	GM19099	blood:	n/a	n/a
24	POLR2A	chr2:86264552-86264687	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:86264283-86264658	K562	blood:	n/a	n/a
26	FOS	chr2:86264372-86264884	HUVEC	blood vessel:	n/a	chr2:86264631-86264639 chr2:86264629-86264641 chr2:86264629-86264640 chr2:86264630-86264640
27	MYC	chr2:86264582-86264782	NB4	blood:	n/a	n/a
28	FOS	chr2:86264600-86264723	MCF10A-Er-Src	breast:	n/a	chr2:86264631-86264639 chr2:86264629-86264641 chr2:86264629-86264640 chr2:86264630-86264640
29	POLR2A	chr2:86264254-86264665	HepG2	liver:	n/a	n/a
30	MYC	chr2:86264460-86264800	HUVEC	blood vessel:	n/a	n/a
31	MTA3	chr2:86262587-86264915	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:86264229-86264909	HUVEC	blood vessel:	n/a	n/a
33	FOS	chr2:86264568-86264718	MCF10A-Er-Src	breast:	n/a	chr2:86264631-86264639 chr2:86264629-86264641 chr2:86264629-86264640 chr2:86264630-86264640
34	POLR2A	chr2:86264225-86264784	GM12892	blood:	n/a	n/a
35	EBF1	chr2:86262933-86264895	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:86264252-86264843	GM12878	blood:	n/a	n/a
37	RAD21	chr2:86264509-86264937	IMR90	lung:	n/a	chr2:86264580-86264592 chr2:86264756-86264768

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10173155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[ASN][1000 genomes]
rs10208184	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1036553	0.95[ASN][1000 genomes]
rs1050301	0.80[ASN][1000 genomes]
rs11127016	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11900161	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17584697	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2059352	0.84[ASN][1000 genomes]
rs2083168	0.89[ASN][1000 genomes]
rs2099616	0.89[ASN][1000 genomes]
rs2099617	0.89[ASN][1000 genomes]
rs2194486	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2241432	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2276626	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2288122	0.82[CHB][hapmap]
rs2303338	1.00[CHB][hapmap]
rs2886885	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs311564	0.94[ASN][1000 genomes]
rs311576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs311578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs311579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs311585	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs311588	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731818	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs3764949	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs3764950	0.93[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3821017	0.90[CHB][hapmap]
rs4344936	0.82[ASN][1000 genomes]
rs4832233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs4832240	0.82[ASN][1000 genomes]
rs6547653	0.88[ASN][1000 genomes]
rs6547654	0.88[ASN][1000 genomes]
rs6547655	0.91[ASN][1000 genomes]
rs6725046	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6731358	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs72847885	0.82[ASN][1000 genomes]
rs7571529	0.87[ASN][1000 genomes]
rs7586985	0.84[ASN][1000 genomes]
rs7595420	0.89[ASN][1000 genomes]
rs7599326	0.86[ASN][1000 genomes]
rs7606897	0.85[ASN][1000 genomes]
rs7607138	0.88[ASN][1000 genomes]
rs879649	0.97[ASN][1000 genomes]
rs893442	0.89[ASN][1000 genomes]
rs934829	0.89[ASN][1000 genomes]
rs934831	0.89[ASN][1000 genomes]
rs965636	0.89[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs717144	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs717144	IMMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86267800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:86258200-86265400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:86260200-86266200	Genic enhancers	Fetal Stomach	stomach
15	chr2:86260600-86265000	Enhancers	Fetal Heart	heart
16	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:86260800-86268800	Weak transcription	Ovary	ovary
19	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:86261400-86265600	Enhancers	Left Ventricle	heart
21	chr2:86261400-86266200	Enhancers	Psoas Muscle	Psoas
22	chr2:86261600-86265600	Enhancers	Right Ventricle	heart
23	chr2:86261800-86266400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:86262000-86265800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:86262400-86265200	Enhancers	Spleen	Spleen
26	chr2:86262400-86265200	Genic enhancers	NHEK	skin
27	chr2:86262400-86266000	Genic enhancers	Brain Angular Gyrus	brain
28	chr2:86262400-86266000	Genic enhancers	Fetal Intestine Small	intestine
29	chr2:86262400-86266000	Enhancers	Right Atrium	heart
30	chr2:86262400-86266200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:86262400-86266200	Enhancers	Lung	lung
32	chr2:86262400-86266800	Genic enhancers	Placenta	Placenta
33	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus
34	chr2:86262600-86264800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:86262600-86264800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:86262600-86265200	Enhancers	Fetal Kidney	kidney
37	chr2:86262600-86265600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:86262600-86265600	Genic enhancers	Brain Germinal Matrix	brain
39	chr2:86262600-86265600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:86262600-86265800	Enhancers	Colon Smooth Muscle	Colon
41	chr2:86262600-86265800	Enhancers	Small Intestine	intestine
42	chr2:86262600-86266200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:86262600-86266200	Enhancers	Stomach Mucosa	stomach
44	chr2:86262600-86266200	Genic enhancers	NHLF	lung
45	chr2:86262600-86267000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:86262800-86264800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:86262800-86265200	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr2:86262800-86265200	Flanking Active TSS	Dnd41	blood
49	chr2:86262800-86265400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:86262800-86265400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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