Variant report

Variant	rs9847948
Chromosome Location	chr3:195887205-195887206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195806334..195810034-chr3:195885466..195888371,4	MCF-7	breast:
2	chr3:195885531..195888308-chr3:195908401..195910834,2	K562	blood:
3	chr3:195806752..195808897-chr3:195887044..195888588,2	K562	blood:
4	chr3:195806752..195810300-chr3:195885348..195891708,10	K562	blood:
5	chr3:195886180..195890208-chr3:195892653..195895699,4	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC069257.9.1-2	chr3:195886771-195887761	ENSG00000224652
2	lnc-AC069257.9.1-2	chr3:195886771-195887593	NONHSAT094297

No data

Variant related genes	Relation type
ENSG00000072274	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12629388	0.86[CEU][hapmap]
rs13068984	0.86[CEU][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs13318003	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13325411	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4261911	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4261912	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4927875	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4927876	0.81[EUR][1000 genomes]
rs4927877	0.81[EUR][1000 genomes]
rs4927880	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4927881	0.87[AFR][1000 genomes]
rs61354401	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61381197	0.81[EUR][1000 genomes]
rs62410503	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62410504	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62410507	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583292	0.81[EUR][1000 genomes]
rs6583296	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs7372337	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7372858	0.80[EUR][1000 genomes]
rs7373119	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7373402	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7613750	0.86[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7617332	0.81[EUR][1000 genomes]
rs9823278	0.81[EUR][1000 genomes]
rs9841719	0.87[AFR][1000 genomes]
rs9841824	0.80[EUR][1000 genomes]
rs9846651	0.87[AFR][1000 genomes]
rs9849726	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9852602	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854867	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9866504	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874982	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876523	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878997	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9884020	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv1002584	chr3:195734933-195910772	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv532214	chr3:195762648-195916068	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv461130	chr3:195776240-195907653	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv593069	chr3:195776240-195907653	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv1005558	chr3:195789462-195919077	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	nsv536890	chr3:195789462-195919077	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv998042	chr3:195840858-195934070	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv878173	chr3:195848264-195889626	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
18	nsv593070	chr3:195854279-195924203	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv878174	chr3:195858887-195949541	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
21	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
22	nsv1004194	chr3:195864466-195919077	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv536891	chr3:195864466-195919077	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
25	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
26	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
27	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195874200-195892000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:195883400-195904400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:195884600-195887600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:195885600-195888000	Enhancers	Fetal Thymus	thymus
5	chr3:195886400-195887600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:195886400-195887600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:195886400-195887800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:195886400-195887800	Enhancers	Primary B cells from cord blood	blood
9	chr3:195886400-195888000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:195886400-195888200	Enhancers	Stomach Mucosa	stomach
11	chr3:195886600-195887400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:195886600-195887400	Enhancers	Gastric	stomach
13	chr3:195886600-195887400	Enhancers	Pancreas	Pancrea
14	chr3:195886600-195887400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr3:195886600-195887600	Enhancers	Adipose Nuclei	Adipose
16	chr3:195886600-195887600	Enhancers	Liver	Liver
17	chr3:195886600-195887600	Enhancers	Colonic Mucosa	Colon
18	chr3:195886600-195887600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:195886600-195887600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr3:195886600-195887600	Flanking Active TSS	Dnd41	blood
21	chr3:195886600-195887800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:195886600-195887800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:195886600-195887800	Enhancers	Small Intestine	intestine
24	chr3:195886600-195887800	Enhancers	GM12878-XiMat	blood
25	chr3:195886600-195888000	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:195886600-195888000	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:195886600-195888000	Enhancers	Fetal Intestine Large	intestine
28	chr3:195886600-195888000	Enhancers	Fetal Intestine Small	intestine
29	chr3:195886600-195888000	Enhancers	Thymus	Thymus
30	chr3:195886800-195887400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:195886800-195887400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:195886800-195887400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:195886800-195887400	Enhancers	Fetal Lung	lung
34	chr3:195886800-195887400	Enhancers	Fetal Muscle Leg	muscle
35	chr3:195886800-195887600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:195886800-195887600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:195886800-195887600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:195886800-195887600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr3:195886800-195887600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:195886800-195887600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:195886800-195887600	Enhancers	Brain Anterior Caudate	brain
42	chr3:195886800-195887600	Enhancers	Fetal Kidney	kidney
43	chr3:195886800-195887600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:195886800-195887600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:195886800-195887800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:195886800-195887800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:195886800-195888000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:195887000-195887400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:195887000-195887400	Enhancers	Esophagus	oesophagus
50	chr3:195887000-195887600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links