Variant report

Variant	rs61204485
Chromosome Location	chr1:169076200-169076201
allele	C/G
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	UBTF	chr1:169075461-169076391	K562	blood:	n/a	n/a
2	YY1	chr1:169074717-169076226	HepG2	liver:	n/a	chr1:169075170-169075184 chr1:169076011-169076025 chr1:169075340-169075351 chr1:169075310-169075321 chr1:169075317-169075331 chr1:169075343-169075352 chr1:169074975-169074989 chr1:169075943-169075954 chr1:169075346-169075355 chr1:169076186-169076197 chr1:169075466-169075480
3	WRNIP1	chr1:169076027-169077144	GM12878	blood:	n/a	n/a
4	ELF1	chr1:169075877-169076378	GM12878	blood:	n/a	chr1:169076260-169076272
5	POLR2A	chr1:169075834-169076201	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:169074922-169076318	A549	lung:	n/a	n/a
7	POLR2A	chr1:169075297-169076291	Gliobla	brain:	n/a	n/a
8	POLR2A	chr1:169075841-169076226	GM12891	blood:	n/a	n/a
9	YY1	chr1:169075876-169076473	GM12878	blood:	n/a	chr1:169076230-169076244 chr1:169076011-169076025 chr1:169076274-169076283 chr1:169075943-169075954 chr1:169076186-169076197
10	POLR2A	chr1:169074617-169076516	GM19193	blood:	n/a	n/a
11	MAX	chr1:169074556-169076383	H1-hESC	embryonic stem cell:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357
12	BRCA1	chr1:169075531-169076651	Hela-S3	cervix:	n/a	n/a
13	RAD21	chr1:169075944-169076229	H1-hESC	embryonic stem cell:	n/a	n/a
14	POU2F2	chr1:169076162-169076574	GM12878	blood:	n/a	chr1:169076394-169076407 chr1:169076389-169076410 chr1:169076271-169076283
15	SIN3AK20	chr1:169074606-169077295	MCF-7	breast:	n/a	n/a
16	HA-E2F1	chr1:169074633-169076791	MCF-7	breast:	n/a	chr1:169075469-169075479 chr1:169075349-169075358 chr1:169076005-169076019 chr1:169075065-169075074 chr1:169075344-169075354 chr1:169075044-169075054 chr1:169075666-169075675
17	SIN3AK20	chr1:169075112-169076571	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr1:169074739-169077862	Hela-S3	cervix:	n/a	n/a
19	UBTF	chr1:169075393-169076676	K562	blood:	n/a	n/a
20	CHD1	chr1:169075808-169077012	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:169075211-169076229	SK-N-MC	brain:	n/a	n/a
22	RFX5	chr1:169074822-169077754	Hela-S3	cervix:	n/a	chr1:169077634-169077643
23	EP300	chr1:169074558-169076305	ECC-1	luminal epithelium:	n/a	chr1:169075030-169075043 chr1:169075296-169075312 chr1:169076181-169076197 chr1:169076180-169076196 chr1:169076033-169076049 chr1:169075343-169075352
24	TAF1	chr1:169075828-169076424	SK-N-SH	brain:	n/a	n/a
25	MAX	chr1:169074502-169076839	A549	lung:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357
26	PML	chr1:169075147-169076279	GM12878	blood:	n/a	n/a
27	CREB1	chr1:169074714-169076584	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:169074709-169082197	HepG2	liver:	n/a	n/a
29	POU2F2	chr1:169075863-169076568	GM12891	blood:	n/a	chr1:169076394-169076407 chr1:169076389-169076410 chr1:169076271-169076283
30	POLR2A	chr1:169074849-169076398	GM18526	blood:	n/a	n/a
31	POLR2A	chr1:169074786-169076389	A549	lung:	n/a	n/a
32	POLR2A	chr1:169075836-169076212	HCT-116	colon:	n/a	n/a
33	CHD2	chr1:169074867-169077276	Hela-S3	cervix:	n/a	n/a
34	CHD2	chr1:169074964-169076520	GM12878	blood:	n/a	n/a
35	GATA3	chr1:169075775-169076620	T-47D	breast:	n/a	n/a
36	POLR2A	chr1:169074748-169076378	Hela-S3	cervix:	n/a	n/a
37	ZBTB7A	chr1:169076116-169076439	K562	blood:	n/a	n/a
38	CTBP2	chr1:169074352-169076271	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF7L2	chr1:169074796-169076518	HCT-116	colon:	n/a	n/a
40	EP300	chr1:169074698-169076374	SK-N-SH	brain:	n/a	chr1:169075030-169075043 chr1:169075296-169075312 chr1:169076181-169076197 chr1:169076180-169076196 chr1:169076033-169076049 chr1:169075343-169075352
41	POLR2A	chr1:169074689-169076214	H1-hESC	embryonic stem cell:	n/a	n/a
42	SMC3	chr1:169074866-169077305	Hela-S3	cervix:	n/a	chr1:169076006-169076016
43	MAZ	chr1:169074351-169076481	K562	blood:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357
44	POLR2A	chr1:169075850-169076216	GM12891	blood:	n/a	n/a
45	RCOR1	chr1:169075385-169077069	K562	blood:	n/a	n/a
46	TCF7L2	chr1:169074775-169076832	Hela-S3	cervix:	n/a	n/a
47	KAP1	chr1:169076043-169077127	HEK293	kidney:	n/a	n/a
48	POLR2A	chr1:169075085-169076230	ProgFib	skin:	n/a	n/a
49	HMGN3	chr1:169074861-169076468	K562	blood:	n/a	n/a
50	TCF12	chr1:169074677-169076330	ECC-1	luminal epithelium:	n/a	chr1:169075044-169075054 chr1:169075804-169075811 chr1:169075253-169075260

No.	Distal block	Cell Line	Cell type
1	chr1:169055830..169060702-chr1:169073415..169077056,5	MCF-7	breast:
2	chr1:169071736..169074539-chr1:169075134..169076733,2	K562	blood:
3	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
4	chr1:169075329..169076274-chr13:36919346..36920283,2	NB4	blood:
5	chr1:169073666..169076222-chr8:146016630..146018644,2	MCF-7	breast:
6	chr1:169075593..169076555-chr12:8179213..8180108,3	Hela-S3	cervix:
7	chr1:169073990..169076920-chr1:169277266..169279793,2	K562	blood:
8	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:
9	chr1:168865232..168870287-chr1:169075405..169077247,5	MCF-7	breast:
10	chr1:169075800..169076779-chr12:53615044..53615856,2	Hela-S3	cervix:
11	chr1:169075479..169078672-chr1:169335264..169338570,4	MCF-7	breast:

Variant related genes	Relation type
ATP1B1	TF binding region
ENSG00000117475	Chromatin interaction
ENSG00000161016	Chromatin interaction
ENSG00000229612	Chromatin interaction
ENSG00000143156	Chromatin interaction
ENSG00000133104	Chromatin interaction
ENSG00000237707	Chromatin interaction
ENSG00000203601	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10919089	1.00[EUR][1000 genomes]
rs12068499	1.00[EUR][1000 genomes]
rs12077900	1.00[EUR][1000 genomes]
rs12084554	1.00[EUR][1000 genomes]
rs12086569	1.00[EUR][1000 genomes]
rs12088527	1.00[EUR][1000 genomes]
rs16861916	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61255541	1.00[AMR][1000 genomes]
rs6698984	1.00[EUR][1000 genomes]
rs73033741	0.86[AFR][1000 genomes]
rs73033742	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73033743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73042062	1.00[EUR][1000 genomes]
rs975991	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv3323390	chr1:169074353-169076901	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169074000-169078800	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:169074400-169077400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:169074600-169076400	Active TSS	Primary T cells from cord blood	blood
4	chr1:169074600-169077000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:169074600-169077600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:169074600-169077800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:169074600-169077800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:169074600-169078000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:169074800-169076400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:169074800-169076400	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr1:169074800-169076400	Active TSS	Brain Angular Gyrus	brain
12	chr1:169074800-169076400	Active TSS	HSMMtube	muscle
13	chr1:169074800-169076600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:169074800-169076600	Active TSS	A549	lung
15	chr1:169074800-169077000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:169074800-169077000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:169074800-169077000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:169074800-169077000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr1:169074800-169077000	Active TSS	HSMM	muscle
20	chr1:169074800-169077200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:169074800-169077200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:169074800-169077200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:169074800-169077200	Active TSS	Duodenum Mucosa	Duodenum
24	chr1:169074800-169077400	Active TSS	Brain Germinal Matrix	brain
25	chr1:169074800-169077600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:169074800-169078000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr1:169074800-169078000	Active TSS	Ovary	ovary
28	chr1:169074800-169078000	Active TSS	Psoas Muscle	Psoas
29	chr1:169074800-169078200	Active TSS	Small Intestine	intestine
30	chr1:169074800-169078800	Active TSS	Brain Substantia Nigra	brain
31	chr1:169074800-169079000	Active TSS	Fetal Kidney	kidney
32	chr1:169074800-169079200	Active TSS	Brain Hippocampus Middle	brain
33	chr1:169074800-169079400	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:169074800-169079600	Active TSS	Stomach Mucosa	stomach
35	chr1:169074800-169079800	Active TSS	Left Ventricle	heart
36	chr1:169074800-169080400	Active TSS	Right Ventricle	heart
37	chr1:169074800-169080800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:169075000-169076200	Active TSS	Primary B cells from peripheral blood	blood
39	chr1:169075000-169076200	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:169075000-169076200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:169075000-169076200	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:169075000-169076200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:169075000-169076200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:169075000-169076200	Bivalent/Poised TSS	Fetal Stomach	stomach
45	chr1:169075000-169076400	Active TSS	Primary monocytes fromperipheralblood	blood
46	chr1:169075000-169076400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr1:169075000-169076400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:169075000-169076400	Weak transcription	Fetal Heart	heart
49	chr1:169075000-169076400	Active TSS	Fetal Muscle Leg	muscle
50	chr1:169075000-169076400	Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links