Variant report

Variant	rs61373194
Chromosome Location	chr1:247171390-247171391
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	JUND	chr1:247171155-247171815	HepG2	liver:	n/a	n/a
2	ARID3A	chr1:247171269-247171768	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:247170816-247171622	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:247171120-247171428	GM12878	blood:	n/a	n/a
5	SP4	chr1:247171144-247171709	H1-hESC	embryonic stem cell:	n/a	chr1:247171452-247171468
6	POLR2A	chr1:247171099-247171416	GM12878	blood:	n/a	n/a
7	HMGN3	chr1:247170862-247171563	K562	blood:	n/a	n/a
8	POLR2A	chr1:247170800-247171782	PFSK-1	brain:	n/a	n/a
9	TBP	chr1:247170962-247171622	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:247170869-247171945	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:247171083-247171748	NB4	blood:	n/a	n/a
12	SP2	chr1:247171243-247171558	K562	blood:	n/a	chr1:247171379-247171388
13	POLR2A	chr1:247170938-247171588	MCF-7	breast:	n/a	n/a
14	IRF1	chr1:247171156-247171540	K562	blood:	n/a	chr1:247171452-247171466
15	MXI1	chr1:247170966-247171695	HepG2	liver:	n/a	n/a
16	RELA	chr1:247170865-247171578	GM15510	blood:	n/a	n/a
17	RUNX3	chr1:247171168-247171429	GM12878	blood:	n/a	n/a
18	RFX5	chr1:247171031-247171662	HepG2	liver:	n/a	n/a
19	SPI1	chr1:247171197-247171490	GM12891	blood:	n/a	chr1:247171386-247171393
20	SP1	chr1:247170982-247171854	HCT-116	colon:	n/a	chr1:247171455-247171469 chr1:247171454-247171466 chr1:247171454-247171466 chr1:247171455-247171465 chr1:247171455-247171465 chr1:247171456-247171465 chr1:247171455-247171464
21	TBL1XR1	chr1:247170984-247171669	K562	blood:	n/a	n/a
22	MAX	chr1:247170868-247171895	NB4	blood:	n/a	n/a
23	SIN3AK20	chr1:247170822-247171859	SK-N-SH	brain:	n/a	n/a
24	PML	chr1:247171003-247171510	K562	blood:	n/a	n/a
25	HEY1	chr1:247171011-247171687	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:247171102-247171534	K562	blood:	n/a	n/a
27	MAX	chr1:247171177-247171621	K562	blood:	n/a	n/a
28	E2F6	chr1:247170780-247171682	K562	blood:	n/a	chr1:247170935-247170944
29	CHD1	chr1:247171090-247171423	H1-hESC	embryonic stem cell:	n/a	n/a
30	ARID3A	chr1:247171325-247171547	K562	blood:	n/a	n/a
31	MAFK	chr1:247171344-247171557	Hela-S3	cervix:	n/a	n/a
32	MXI1	chr1:247170737-247171610	IMR90	lung:	n/a	n/a
33	STAT3	chr1:247171174-247171708	MCF10A-Er-Src	breast:	n/a	n/a
34	MAX	chr1:247170812-247171631	K562	blood:	n/a	n/a
35	TAF1	chr1:247170877-247171538	HepG2	liver:	n/a	n/a
36	PBX3	chr1:247171290-247171588	GM12878	blood:	n/a	chr1:247171517-247171526 chr1:247171474-247171483
37	MAZ	chr1:247170887-247171648	K562	blood:	n/a	n/a
38	MYC	chr1:247171332-247171398	K562	blood:	n/a	n/a
39	MYC	chr1:247170988-247171638	MCF10A-Er-Src	breast:	n/a	n/a
40	GABPA	chr1:247171190-247171579	Hela-S3	cervix:	n/a	n/a
41	YY1	chr1:247170883-247171641	ECC-1	luminal epithelium:	n/a	chr1:247170932-247170946 chr1:247171022-247171036
42	GABPA	chr1:247170970-247171731	SK-N-SH	brain:	n/a	n/a
43	NFYA	chr1:247170927-247171842	Hela-S3	cervix:	n/a	chr1:247171405-247171418
44	POLR2A	chr1:247171159-247171455	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr1:247171151-247171413	HepG2	liver:	n/a	n/a
46	GTF2F1	chr1:247171146-247171634	Hela-S3	cervix:	n/a	n/a
47	SP1	chr1:247171116-247171771	A549	lung:	n/a	chr1:247171455-247171469 chr1:247171454-247171466 chr1:247171454-247171466 chr1:247171455-247171465 chr1:247171455-247171465 chr1:247171456-247171465 chr1:247171455-247171464
48	GABPA	chr1:247171231-247171436	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:247170744-247171716	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr1:247169956-247171641	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247169768..247172852-chr1:247266315..247269719,3	K562	blood:
2	chr1:247170899..247171471-chr5:36606529..36607214,2	Hela-S3	cervix:
3	chr1:247093628..247096678-chr1:247168698..247172076,4	MCF-7	breast:
4	chr1:247170921..247172935-chr1:247241527..247243070,2	MCF-7	breast:
5	chr1:247169673..247172319-chr1:247241987..247243991,2	K562	blood:
6	chr1:247170817..247171398-chr3:194980386..194981232,2	Hela-S3	cervix:
7	chr1:247093881..247096879-chr1:247169993..247171703,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AHCTF1-3	chr1:247171208-247171395	NR_037892

Variant related genes	Relation type
ZNF695	TF binding region
ENSG00000079215	Chromatin interaction
ENSG00000188295	Chromatin interaction
ENSG00000135747	Chromatin interaction
ENSG00000173950	Chromatin interaction
ENSG00000153207	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10802462	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924892	1.00[ASN][1000 genomes]
rs10924895	1.00[ASN][1000 genomes]
rs10924896	1.00[ASN][1000 genomes]
rs10924897	1.00[ASN][1000 genomes]
rs10924899	1.00[ASN][1000 genomes]
rs1112137	1.00[ASN][1000 genomes]
rs12060791	1.00[ASN][1000 genomes]
rs12116484	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118487	1.00[ASN][1000 genomes]
rs12120876	0.82[EUR][1000 genomes]
rs12122044	1.00[ASN][1000 genomes]
rs12122047	1.00[ASN][1000 genomes]
rs12122290	1.00[ASN][1000 genomes]
rs12123948	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130075	1.00[ASN][1000 genomes]
rs12131419	1.00[ASN][1000 genomes]
rs12135842	1.00[ASN][1000 genomes]
rs12135986	1.00[ASN][1000 genomes]
rs12139893	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141232	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141355	1.00[ASN][1000 genomes]
rs12142305	1.00[ASN][1000 genomes]
rs12144260	1.00[ASN][1000 genomes]
rs1565897	1.00[ASN][1000 genomes]
rs1573897	1.00[ASN][1000 genomes]
rs2055191	1.00[ASN][1000 genomes]
rs2055192	1.00[ASN][1000 genomes]
rs2172973	1.00[ASN][1000 genomes]
rs2379189	0.86[EUR][1000 genomes]
rs2380113	1.00[ASN][1000 genomes]
rs2642957	0.83[EUR][1000 genomes]
rs2642974	0.83[EUR][1000 genomes]
rs2642978	0.83[EUR][1000 genomes]
rs2818872	0.83[EUR][1000 genomes]
rs2818874	0.87[EUR][1000 genomes]
rs2818893	0.83[EUR][1000 genomes]
rs28540229	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28614003	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310567	1.00[ASN][1000 genomes]
rs4319379	1.00[ASN][1000 genomes]
rs4634944	1.00[ASN][1000 genomes]
rs4925540	1.00[ASN][1000 genomes]
rs4925622	1.00[ASN][1000 genomes]
rs4971315	1.00[ASN][1000 genomes]
rs4971316	1.00[ASN][1000 genomes]
rs4971317	1.00[ASN][1000 genomes]
rs4971319	1.00[ASN][1000 genomes]
rs55984722	1.00[ASN][1000 genomes]
rs56884994	1.00[ASN][1000 genomes]
rs59525684	1.00[ASN][1000 genomes]
rs61498462	1.00[ASN][1000 genomes]
rs61852608	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852610	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852630	1.00[ASN][1000 genomes]
rs61852637	1.00[ASN][1000 genomes]
rs61852638	1.00[ASN][1000 genomes]
rs61852639	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61852640	1.00[ASN][1000 genomes]
rs61852641	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61852642	1.00[ASN][1000 genomes]
rs61852646	0.90[AMR][1000 genomes]
rs6426214	1.00[ASN][1000 genomes]
rs6426216	1.00[ASN][1000 genomes]
rs6657686	1.00[ASN][1000 genomes]
rs6664217	1.00[ASN][1000 genomes]
rs6689229	1.00[ASN][1000 genomes]
rs6701582	1.00[ASN][1000 genomes]
rs72768397	1.00[ASN][1000 genomes]
rs7418825	1.00[ASN][1000 genomes]
rs7511962	1.00[ASN][1000 genomes]
rs7512099	1.00[ASN][1000 genomes]
rs7512150	1.00[ASN][1000 genomes]
rs7513678	1.00[ASN][1000 genomes]
rs7518427	1.00[ASN][1000 genomes]
rs7519795	1.00[ASN][1000 genomes]
rs7521422	1.00[ASN][1000 genomes]
rs7522300	1.00[ASN][1000 genomes]
rs7526191	1.00[ASN][1000 genomes]
rs7535251	1.00[ASN][1000 genomes]
rs7535264	1.00[ASN][1000 genomes]
rs7542852	1.00[ASN][1000 genomes]
rs7543803	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546342	1.00[ASN][1000 genomes]
rs7546777	1.00[ASN][1000 genomes]
rs7547915	1.00[ASN][1000 genomes]
rs7549105	1.00[ASN][1000 genomes]
rs7549410	1.00[ASN][1000 genomes]
rs7549531	1.00[ASN][1000 genomes]
rs7551896	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers 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	42 gene(s)	inside rSNPs	diseases
5	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv549546	chr1:247145690-247205056	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv945436	chr1:247162782-247171728	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv3368851	chr1:247170017-247195360	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61373194	LOC729810	cis	frontal cortex	BrainEAC

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247169800-247171800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:247169800-247171800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:247169800-247171800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:247169800-247172000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:247169800-247172000	Active TSS	Hela-S3	cervix
6	chr1:247170000-247171400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:247170000-247171400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:247170000-247171400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:247170000-247171400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:247170000-247171400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:247170000-247171400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:247170000-247171400	ZNF genes & repeats	Liver	Liver
13	chr1:247170000-247171600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:247170000-247171600	Active TSS	NH-A	brain
15	chr1:247170000-247171800	Active TSS	Brain Germinal Matrix	brain
16	chr1:247170000-247171800	Active TSS	Duodenum Mucosa	Duodenum
17	chr1:247170000-247171800	Active TSS	HSMM	muscle
18	chr1:247170000-247171800	Active TSS	NHDF-Ad	bronchial
19	chr1:247170000-247172000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:247170200-247171400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr1:247170200-247171400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:247170200-247171400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:247170200-247171600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr1:247170200-247171800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:247170200-247171800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:247170200-247171800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr1:247170200-247171800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:247170200-247171800	Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:247170200-247171800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:247170200-247171800	Active TSS	HSMMtube	muscle
31	chr1:247170200-247171800	Active TSS	Osteobl	bone
32	chr1:247170400-247171400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:247170400-247171400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:247170400-247171400	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr1:247170400-247171600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:247170400-247171600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:247170400-247171600	Active TSS	Right Atrium	heart
38	chr1:247170400-247171600	Active TSS	HUVEC	blood vessel
39	chr1:247170400-247171600	Active TSS	K562	blood
40	chr1:247170400-247171800	Active TSS	H1 Cell Line	embryonic stem cell
41	chr1:247170400-247171800	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:247170400-247171800	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:247170400-247171800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:247170400-247171800	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr1:247170400-247171800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:247170400-247171800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:247170400-247171800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:247170400-247171800	Active TSS	Fetal Muscle Leg	muscle
49	chr1:247170400-247171800	Active TSS	Fetal Stomach	stomach
50	chr1:247170400-247171800	Active TSS	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links