Variant report

Variant	rs3810827
Chromosome Location	chr2:86334386-86334387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:86331775-86334815	SK-N-SH	brain:	n/a	n/a
2	MYC	chr2:86334215-86334415	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr2:86332360-86334572	SK-N-SH	brain:	n/a	chr2:86333509-86333519 chr2:86334349-86334358
4	MTA3	chr2:86332435-86334391	GM12878	blood:	n/a	n/a
5	IRF1	chr2:86334050-86334490	K562	blood:	n/a	n/a
6	POLR2A	chr2:86332385-86334609	PBDE	blood:	n/a	n/a
7	RELA	chr2:86332424-86334605	GM18505	blood:	n/a	n/a
8	HCFC1	chr2:86332055-86334717	Hela-S3	cervix:	n/a	n/a
9	YY1	chr2:86334195-86334460	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:86332400-86334991	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:86332451-86334428	GM12878	blood:	n/a	n/a
12	CHD1	chr2:86332235-86334446	IMR90	lung:	n/a	n/a
13	SREBP1	chr2:86332135-86335428	GM12878	blood:	n/a	n/a
14	STAT3	chr2:86334225-86334394	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:86332318-86334588	GM12891	blood:	n/a	n/a
16	POLR2A	chr2:86332484-86334419	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86332345..86334570-chr2:86419598..86423755,4	MCF-7	breast:
2	chr2:86331787..86335346-chr2:86347358..86351403,5	K562	blood:
3	chr2:86075421..86077051-chr2:86332502..86335469,2	K562	blood:
4	chr2:86043786..86048456-chr2:86331469..86335365,4	MCF-7	breast:
5	chr2:86329731..86334667-chr2:86420655..86424478,8	K562	blood:
6	chr2:86333093..86335587-chr2:86356462..86359498,3	K562	blood:
7	chr2:86332781..86335214-chr2:86396440..86398251,2	K562	blood:
8	chr2:86330519..86334714-chr2:86420374..86424108,6	K562	blood:

No data

Variant related genes	Relation type
PTCD3	TF binding region
POLR1A	TF binding region
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction
ENSG00000132300	Chromatin interaction
ENSG00000265420	Chromatin interaction
ENSG00000252321	Chromatin interaction
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10165327	0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10168635	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10174095	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10179090	0.89[ASN][1000 genomes]
rs1019591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1036554	0.91[ASN][1000 genomes]
rs10427394	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11899576	0.91[ASN][1000 genomes]
rs12612513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617717	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12620810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621992	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12622009	0.92[ASN][1000 genomes]
rs12622715	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs12624126	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13384563	0.89[ASN][1000 genomes]
rs13390702	0.91[ASN][1000 genomes]
rs1559516	0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1561328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026854	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17027011	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17584578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17618001	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2018608	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2164879	0.92[ASN][1000 genomes]
rs2241435	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2241437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278085	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278086	1.00[AMR][1000 genomes]
rs2278087	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288121	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2289237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2303339	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2303340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311562	0.87[ASN][1000 genomes]
rs311566	0.87[ASN][1000 genomes]
rs311567	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs34522092	0.86[ASN][1000 genomes]
rs3731819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770066	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770081	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770087	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs3770089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3770090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3815840	0.87[ASN][1000 genomes]
rs4832242	0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4832250	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs56104203	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326127	0.86[ASN][1000 genomes]
rs56977454	0.86[ASN][1000 genomes]
rs57083584	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57398459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58186343	0.88[ASN][1000 genomes]
rs58365138	0.86[ASN][1000 genomes]
rs58898686	0.88[ASN][1000 genomes]
rs59835600	0.84[ASN][1000 genomes]
rs59947468	1.00[AMR][1000 genomes]
rs60479377	1.00[AMR][1000 genomes]
rs60649958	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60719866	1.00[AMR][1000 genomes]
rs6750765	0.95[ASN][1000 genomes]
rs73943946	0.91[ASN][1000 genomes]
rs73947314	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608262	0.90[ASN][1000 genomes]
rs9789563	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9973880	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats 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
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer 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
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS 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
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS 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
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS 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
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS 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
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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 miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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
16	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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 miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86330600-86334600	Active TSS	GM12878-XiMat	blood
2	chr2:86330800-86335400	Active TSS	Psoas Muscle	Psoas
3	chr2:86331000-86334400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:86331200-86334800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr2:86331400-86334400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:86331400-86334400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:86331400-86334400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:86331400-86334800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:86331400-86335400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:86331600-86334400	Active TSS	HMEC	breast
11	chr2:86331800-86334400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:86331800-86334400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:86331800-86334400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:86331800-86334600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:86331800-86334600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:86332000-86334400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr2:86332000-86334400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:86332000-86334400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr2:86332000-86334400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:86332000-86334400	Active TSS	Fetal Intestine Small	intestine
21	chr2:86332000-86334400	Active TSS	Fetal Muscle Trunk	muscle
22	chr2:86332000-86334600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:86332000-86334600	Active TSS	H9 Cell Line	embryonic stem cell
24	chr2:86332000-86334600	Active TSS	Colonic Mucosa	Colon
25	chr2:86332000-86334600	Active TSS	Fetal Muscle Leg	muscle
26	chr2:86332000-86334600	Active TSS	Right Atrium	heart
27	chr2:86332000-86334800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:86332000-86335000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:86332200-86334400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:86332200-86334400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:86332200-86334400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:86332200-86334400	Active TSS	Esophagus	oesophagus
33	chr2:86332200-86334400	Active TSS	A549	lung
34	chr2:86332200-86334600	Active TSS	Fetal Intestine Large	intestine
35	chr2:86332200-86334800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:86333600-86334400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr2:86333600-86334400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr2:86333600-86334600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr2:86333600-86334600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr2:86333600-86334800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:86333800-86334400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:86333800-86334400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr2:86333800-86334400	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr2:86333800-86334400	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr2:86333800-86334400	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr2:86333800-86334400	Enhancers	Spleen	Spleen
47	chr2:86333800-86334600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr2:86333800-86334600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr2:86333800-86334600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr2:86333800-86334600	Flanking Active TSS	Fetal Brain Male	brain

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