Variant report

Variant	rs916295
Chromosome Location	chr6:36725464-36725465
allele	A/C
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	chr6:36722910-36725515	GM12891	blood:	n/a	n/a
2	IKZF1	chr6:36724490-36725561	GM12878	blood:	n/a	n/a
3	RELA	chr6:36724567-36725635	GM19099	blood:	n/a	n/a
4	POLR2A	chr6:36723030-36725560	Raji	blood:	n/a	n/a
5	CTCF	chr6:36725420-36725570	GM12874	blood:	n/a	n/a
6	MTA3	chr6:36722921-36725652	GM12878	blood:	n/a	n/a
7	RELA	chr6:36724312-36725632	GM18505	blood:	n/a	n/a
8	SMC3	chr6:36725075-36725569	GM12878	blood:	n/a	n/a
9	RELA	chr6:36722482-36725569	GM12891	blood:	n/a	chr6:36723710-36723719 chr6:36723710-36723719
10	CTCF	chr6:36725400-36725550	GM12871	blood:	n/a	n/a
11	RELA	chr6:36722522-36725483	GM12878	blood:	n/a	chr6:36723710-36723719 chr6:36723710-36723719
12	CTCF	chr6:36725440-36725590	GM12875	blood:	n/a	n/a
13	POLR2A	chr6:36722703-36725539	GM12878	blood:	n/a	n/a
14	RELA	chr6:36724346-36725536	GM10847	blood:	n/a	n/a
15	RELA	chr6:36723377-36725569	GM18951	blood:	n/a	chr6:36723710-36723719 chr6:36723710-36723719
16	RELA	chr6:36724552-36725681	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36560234..36563233-chr6:36722828..36725947,3	MCF-7	breast:
2	chr6:36561839..36564756-chr6:36723772..36727529,4	MCF-7	breast:
3	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
4	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
5	chr6:36724390..36726745-chr6:36953555..36956553,2	K562	blood:

Variant related genes	Relation type
CPNE5	TF binding region
ENSG00000112081	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10807175	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947628	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12198675	0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13193217	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs13203743	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236426	0.89[ASN][1000 genomes]
rs236445	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4557518	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs763047	0.85[YRI][hapmap]
rs763048	0.96[YRI][hapmap]
rs916297	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs916304	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9380596	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs9380598	0.90[ASN][1000 genomes]

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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs916295	MAPK14	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36709200-36727000	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:36718600-36725800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:36718600-36726600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:36718800-36726800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:36718800-36727400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:36718800-36727400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:36719600-36725800	Enhancers	HUVEC	blood vessel
8	chr6:36719600-36727000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:36719800-36725600	Enhancers	Spleen	Spleen
10	chr6:36719800-36726000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:36720000-36726200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:36720200-36726400	Weak transcription	Pancreas	Pancrea
13	chr6:36720600-36725600	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:36720600-36726400	Weak transcription	HMEC	breast
15	chr6:36721200-36726600	Weak transcription	Brain Anterior Caudate	brain
16	chr6:36721200-36726600	Weak transcription	Fetal Heart	heart
17	chr6:36721200-36726600	Weak transcription	HSMMtube	muscle
18	chr6:36721400-36726400	Weak transcription	Fetal Intestine Large	intestine
19	chr6:36721400-36726600	Weak transcription	Fetal Intestine Small	intestine
20	chr6:36721400-36728600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:36721800-36725600	Enhancers	Fetal Thymus	thymus
22	chr6:36721800-36726600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:36721800-36726600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:36721800-36733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:36722400-36725600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr6:36722400-36725600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:36722600-36725800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr6:36722800-36727600	Enhancers	Stomach Mucosa	stomach
29	chr6:36722800-36748200	Weak transcription	Fetal Kidney	kidney
30	chr6:36723200-36725600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr6:36723400-36725600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:36723400-36725600	Enhancers	Adipose Nuclei	Adipose
33	chr6:36723600-36726600	Enhancers	Placenta	Placenta
34	chr6:36723800-36726600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:36723800-36726800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:36723800-36727400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:36723800-36736200	Weak transcription	Right Atrium	heart
38	chr6:36724000-36726600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:36724000-36728200	Weak transcription	Fetal Stomach	stomach
40	chr6:36724000-36736200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:36724200-36726200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr6:36724200-36727200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:36724400-36726600	Weak transcription	A549	lung
44	chr6:36724400-36726800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:36724600-36726000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:36724800-36725600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:36724800-36725800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:36724800-36726000	Enhancers	Colonic Mucosa	Colon
49	chr6:36724800-36726400	Weak transcription	Esophagus	oesophagus
50	chr6:36724800-36726400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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