Variant report

Variant	rs2041527
Chromosome Location	chr7:117825834-117825835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:116897859..116900656-chr7:117824567..117826449,2	K562	blood:
2	chr7:117825039..117827152-chr7:120589846..120592123,2	MCF-7	breast:
3	chr7:117824273..117825955-chr7:117864602..117866522,2	MCF-7	breast:
4	chr7:117825257..117827852-chr7:118309009..118311377,2	K562	blood:

Variant related genes	Relation type
ENSG00000106013	Chromatin interaction
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1015782	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10226152	0.81[EUR][1000 genomes]
rs10227326	0.81[EUR][1000 genomes]
rs10229589	0.81[EUR][1000 genomes]
rs10247768	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10487390	0.81[EUR][1000 genomes]
rs1054032	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1061731	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs11486992	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs11487110	0.88[CEU][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11542074	0.81[EUR][1000 genomes]
rs11543742	0.81[EUR][1000 genomes]
rs11974039	0.81[CEU][hapmap]
rs11979012	0.84[CEU][hapmap]
rs12670769	0.91[EUR][1000 genomes]
rs1544583	0.85[EUR][1000 genomes]
rs1544584	0.80[EUR][1000 genomes]
rs17140984	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs17141053	0.81[CEU][hapmap]
rs2058418	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2215628	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2286863	0.81[EUR][1000 genomes]
rs2286865	0.81[CEU][hapmap]
rs2402322	0.81[EUR][1000 genomes]
rs2896242	0.81[EUR][1000 genomes]
rs33924981	0.81[EUR][1000 genomes]
rs34019303	0.81[EUR][1000 genomes]
rs41944	0.82[EUR][1000 genomes]
rs45604739	0.81[EUR][1000 genomes]
rs4730837	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs5002232	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs5002233	0.81[EUR][1000 genomes]
rs61328879	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62466515	0.81[EUR][1000 genomes]
rs6466648	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6942513	0.87[CEU][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6944524	0.81[EUR][1000 genomes]
rs6946855	0.84[CEU][hapmap]
rs6948096	0.81[EUR][1000 genomes]
rs6964911	0.96[CEU][hapmap]
rs6965144	0.81[EUR][1000 genomes]
rs769435	0.88[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7786233	0.88[CEU][hapmap]
rs7796145	0.81[EUR][1000 genomes]
rs7796148	0.81[EUR][1000 genomes]
rs7797855	0.81[EUR][1000 genomes]
rs9641593	0.80[EUR][1000 genomes]
rs9655829	0.84[CEU][hapmap];0.83[MKK][hapmap];0.81[EUR][1000 genomes]
rs9656259	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs979652	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2041527	KCND2	cis	parietal	SCAN
rs2041527	NAA38	cis	lymphoblastoid	seeQTL
rs2041527	LSM8	cis	multi-tissue	Pritchard
rs2041527	ANKRD7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117823000-117826000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:117823000-117826000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:117823200-117826000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:117823400-117826000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:117823400-117826000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr7:117823400-117826000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr7:117823400-117826000	Active TSS	Fetal Brain Female	brain
8	chr7:117823400-117826800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:117823600-117826600	Active TSS	K562	blood
10	chr7:117824600-117826000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr7:117824800-117826000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr7:117824800-117826000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr7:117824800-117826000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:117824800-117826000	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr7:117824800-117829000	Weak transcription	Lung	lung
16	chr7:117824800-117829200	Weak transcription	Gastric	stomach
17	chr7:117824800-117832600	Weak transcription	Pancreas	Pancrea
18	chr7:117825000-117826000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr7:117825000-117826000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr7:117825000-117826000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:117825000-117826000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr7:117825000-117826000	Enhancers	Fetal Brain Male	brain
23	chr7:117825000-117826000	Enhancers	Small Intestine	intestine
24	chr7:117825000-117826200	Enhancers	Primary B cells from peripheral blood	blood
25	chr7:117825000-117826200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr7:117825000-117826600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:117825000-117827000	Weak transcription	Placenta	Placenta
28	chr7:117825000-117827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:117825000-117830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:117825000-117834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
32	chr7:117825200-117826000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr7:117825200-117826000	Enhancers	Primary hematopoietic stem cells	blood
34	chr7:117825200-117826000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:117825200-117826000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr7:117825200-117826000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr7:117825200-117826000	Enhancers	Right Atrium	heart
38	chr7:117825200-117826000	Enhancers	Stomach Mucosa	stomach
39	chr7:117825200-117826200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr7:117825200-117826200	Flanking Active TSS	NHEK	skin
41	chr7:117825200-117826400	Enhancers	Brain Angular Gyrus	brain
42	chr7:117825200-117826800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:117825200-117826800	Enhancers	Colon Smooth Muscle	Colon
44	chr7:117825200-117826800	Enhancers	Fetal Heart	heart
45	chr7:117825200-117827000	Enhancers	Primary B cells from cord blood	blood
46	chr7:117825200-117827000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:117825200-117828000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr7:117825200-117828400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr7:117825200-117830600	Weak transcription	HSMMtube	muscle
50	chr7:117825200-117834000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links