Variant report

Variant	rs4135036
Chromosome Location	chr12:104359054-104359055
allele	C/T
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	HCFC1	chr12:104358419-104361266	Hela-S3	cervix:	n/a	n/a
2	KAP1	chr12:104358843-104359847	U2OS	brain:	n/a	n/a
3	POLR2A	chr12:104358808-104360710	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:104358839-104360225	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:104358245-104360335	K562	blood:	n/a	n/a
6	POLR2A	chr12:104358891-104360241	K562	blood:	n/a	n/a
7	POLR2A	chr12:104359051-104360395	U87	brain:	n/a	n/a
8	POLR2A	chr12:104358877-104360387	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:104359033-104360377	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:104358932-104360391	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr12:104358597-104361078	MCF10A-Er-Src	breast:	n/a	n/a
12	TAF1	chr12:104358947-104360317	A549	lung:	n/a	n/a
13	MYC	chr12:104358618-104360631	A549	lung:	n/a	chr12:104359744-104359751 chr12:104359568-104359577 chr12:104358870-104358879 chr12:104359407-104359416 chr12:104359568-104359577
14	POLR2A	chr12:104358246-104360260	GM19099	blood:	n/a	n/a
15	REST	chr12:104359031-104360408	A549	lung:	n/a	chr12:104360178-104360198 chr12:104359845-104359858 chr12:104359393-104359402
16	EP300	chr12:104358917-104360372	A549	lung:	n/a	chr12:104359765-104359781
17	YY1	chr12:104358659-104360356	GM12878	blood:	n/a	chr12:104359847-104359861 chr12:104358861-104358870
18	POLR2A	chr12:104358803-104360393	GM12878	blood:	n/a	n/a
19	RFX5	chr12:104359052-104360112	Hela-S3	cervix:	n/a	n/a
20	MAZ	chr12:104358383-104360788	IMR90	lung:	n/a	chr12:104359744-104359751 chr12:104359568-104359577 chr12:104358870-104358879 chr12:104359407-104359416 chr12:104359568-104359577
21	POLR2A	chr12:104358691-104360222	K562	blood:	n/a	n/a
22	ZC3H11A	chr12:104358867-104359724	K562	blood:	n/a	n/a
23	POLR2A	chr12:104358925-104360274	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:104358983-104360245	MCF-7	breast:	n/a	n/a
25	POLR2A	chr12:104358052-104360401	PFSK-1	brain:	n/a	n/a
26	MAFF	chr12:104358843-104359537	K562	blood:	n/a	n/a
27	CHD1	chr12:104358841-104360867	H1-hESC	embryonic stem cell:	n/a	n/a
28	STAT3	chr12:104358888-104359181	MCF10A-Er-Src	breast:	n/a	n/a
29	USF2	chr12:104358623-104359811	Hela-S3	cervix:	n/a	chr12:104359568-104359577 chr12:104359566-104359577 chr12:104359568-104359577 chr12:104359566-104359579 chr12:104359569-104359578
30	PML	chr12:104358695-104360471	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:104357794-104360395	SK-N-MC	brain:	n/a	n/a
32	USF1	chr12:104359030-104360124	HCT-116	colon:	n/a	chr12:104359568-104359577 chr12:104359568-104359577 chr12:104359566-104359579 chr12:104359569-104359578
33	NFIC	chr12:104358936-104360136	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:104358195-104361110	GM12891	blood:	n/a	n/a
35	POLR2A	chr12:104358724-104360395	U87	brain:	n/a	n/a
36	MTA3	chr12:104359003-104359778	GM12878	blood:	n/a	n/a
37	REST	chr12:104358616-104360557	H1-neurons	neurons:	n/a	chr12:104360178-104360198 chr12:104359845-104359858 chr12:104359393-104359402
38	MAFK	chr12:104359000-104359731	K562	blood:	n/a	chr12:104359446-104359463
39	CHD2	chr12:104359044-104360053	K562	blood:	n/a	n/a
40	POLR2A	chr12:104358980-104360182	GM12892	blood:	n/a	n/a
41	PML	chr12:104358923-104360226	K562	blood:	n/a	n/a
42	E2F6	chr12:104358925-104360115	A549	lung:	n/a	chr12:104359845-104359855 chr12:104359959-104359968
43	MAX	chr12:104358916-104360469	A549	lung:	n/a	chr12:104359744-104359751 chr12:104359568-104359577 chr12:104359407-104359416 chr12:104359568-104359577
44	POLR2A	chr12:104358901-104360365	GM12892	blood:	n/a	n/a
45	MXI1	chr12:104358665-104360949	IMR90	lung:	n/a	n/a
46	BCL3	chr12:104359050-104360242	A549	lung:	n/a	chr12:104359854-104359863 chr12:104359609-104359618 chr12:104359355-104359362 chr12:104359513-104359522
47	POLR2A	chr12:104359019-104360272	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYBL2	chr12:104358974-104360190	HepG2	liver:	n/a	n/a
49	BHLHE40	chr12:104358564-104360073	GM12878	blood:	n/a	chr12:104359568-104359577 chr12:104359568-104359577 chr12:104359566-104359579 chr12:104359569-104359578
50	POLR2A	chr12:104358262-104360391	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104358049..104359986-chr12:104530882..104532737,3	K562	blood:
2	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:
3	chr12:104357850..104359549-chr12:104531019..104533949,2	K562	blood:
4	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
5	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
6	chr12:104358555..104361363-chr12:104388778..104391446,2	MCF-7	breast:
7	chr12:104322943..104325215-chr12:104358408..104360868,4	MCF-7	breast:
8	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:
9	chr12:104298405..104301396-chr12:104359031..104361017,2	K562	blood:
10	chr12:104359049..104360010-chr6:105850675..105851420,2	Hela-S3	cervix:
11	chr12:104233429..104235958-chr12:104358438..104361946,3	MCF-7	breast:
12	chr12:102510855..102512497-chr12:104358534..104361115,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf73-2	chr12:104357568-104359481	NONHSAT030401

Variant related genes	Relation type
TDG	TF binding region
ENSG00000214198	Chromatin interaction
ENSG00000075188	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000085377	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1038497	0.83[JPT][hapmap]
rs10861144	1.00[CEU][hapmap]
rs11111812	1.00[CEU][hapmap]
rs11111819	1.00[CEU][hapmap]
rs11111820	1.00[CEU][hapmap]
rs11111839	1.00[CEU][hapmap]
rs11111842	1.00[CEU][hapmap]
rs11111843	1.00[CEU][hapmap]
rs11111846	1.00[CEU][hapmap]
rs11111869	0.83[ASN][1000 genomes]
rs11111871	0.82[AMR][1000 genomes]
rs1165685	0.82[ASN][1000 genomes]
rs11830285	1.00[CEU][hapmap]
rs11831836	1.00[CEU][hapmap]
rs12228360	1.00[CEU][hapmap]
rs12820602	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1305392	0.93[ASN][1000 genomes]
rs17034916	1.00[CEU][hapmap]
rs17034931	1.00[CEU][hapmap]
rs17034977	0.94[ASN][1000 genomes]
rs2583252	0.92[ASN][1000 genomes]
rs34009709	0.99[ASN][1000 genomes]
rs3751206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135128	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4135137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs58712273	0.94[ASN][1000 genomes]
rs67703341	0.94[ASN][1000 genomes]
rs67908919	0.99[ASN][1000 genomes]
rs7295489	1.00[CEU][hapmap]
rs7300034	0.95[ASN][1000 genomes]
rs73177940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177955	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73177956	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73177961	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1799879	chr12:104351057-104360713	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104357800-104359400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:104357800-104361200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104358000-104359200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr12:104358000-104359400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr12:104358000-104360600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:104358000-104360800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr12:104358200-104359200	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr12:104358200-104359200	Flanking Active TSS	NH-A	brain
9	chr12:104358200-104359400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:104358200-104359400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:104358200-104359400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr12:104358200-104360600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:104358200-104360600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:104358200-104361200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:104358400-104359200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:104358400-104359200	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr12:104358400-104359200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr12:104358400-104359200	Flanking Active TSS	Liver	Liver
19	chr12:104358400-104359200	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr12:104358400-104359200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr12:104358400-104359400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:104358400-104359600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr12:104358400-104360600	Active TSS	Stomach Mucosa	stomach
24	chr12:104358400-104360600	Active TSS	HSMM	muscle
25	chr12:104358400-104360800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:104358400-104360800	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:104358400-104360800	Active TSS	Ovary	ovary
28	chr12:104358400-104361000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:104358400-104361000	Active TSS	Fetal Intestine Large	intestine
30	chr12:104358400-104361200	Active TSS	Psoas Muscle	Psoas
31	chr12:104358600-104359200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr12:104358600-104359200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr12:104358600-104359200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr12:104358600-104359200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:104358600-104359200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr12:104358600-104359200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr12:104358600-104359200	Weak transcription	Spleen	Spleen
38	chr12:104358600-104359200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr12:104358600-104359400	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr12:104358600-104360400	Active TSS	Duodenum Mucosa	Duodenum
41	chr12:104358600-104360400	Active TSS	Fetal Brain Male	brain
42	chr12:104358600-104360400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr12:104358600-104360600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:104358600-104360600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:104358600-104360600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:104358600-104360600	Active TSS	Brain Germinal Matrix	brain
47	chr12:104358600-104360600	Active TSS	Fetal Brain Female	brain
48	chr12:104358600-104360600	Active TSS	Fetal Kidney	kidney
49	chr12:104358600-104360600	Active TSS	Fetal Stomach	stomach
50	chr12:104358600-104360600	Active TSS	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links