Variant report

Variant	rs12461431
Chromosome Location	chr19:39087387-39087388
allele	A/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	HMGN3	chr19:39086874-39087655	K562	blood:	n/a	n/a
2	MAX	chr19:39087361-39087592	K562	blood:	n/a	chr19:39087537-39087547
3	MAX	chr19:39086767-39087788	A549	lung:	n/a	chr19:39087537-39087547 chr19:39086919-39086929
4	E2F6	chr19:39086638-39087693	A549	lung:	n/a	chr19:39086884-39086893 chr19:39087339-39087354 chr19:39087080-39087095
5	UBTF	chr19:39086834-39087484	K562	blood:	n/a	n/a
6	MAX	chr19:39086772-39087477	A549	lung:	n/a	chr19:39086919-39086929
7	MAX	chr19:39086920-39087529	K562	blood:	n/a	n/a
8	SMC3	chr19:39087324-39087419	K562	blood:	n/a	n/a
9	SP4	chr19:39086587-39087717	H1-hESC	embryonic stem cell:	n/a	chr19:39087555-39087571 chr19:39086880-39086896 chr19:39087534-39087550 chr19:39086916-39086932 chr19:39087143-39087154 chr19:39087178-39087194 chr19:39086758-39086774 chr19:39087176-39087192 chr19:39087532-39087548 chr19:39087303-39087319
10	TAL1	chr19:39087309-39087500	K562	blood:	n/a	n/a
11	CHD2	chr19:39087249-39087392	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr19:39086736-39087513	PANC-1	pancreas:	n/a	chr19:39086919-39086932 chr19:39087136-39087149
13	CTCF	chr19:39087303-39087509	K562	blood:	n/a	n/a
14	ELK1	chr19:39087302-39087486	K562	blood:	n/a	n/a
15	POLR2A	chr19:39086443-39087600	H1-hESC	embryonic stem cell:	n/a	n/a
16	JUND	chr19:39086901-39087390	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr19:39087360-39087510	Caco-2	colon:	n/a	n/a
18	CBX3	chr19:39086718-39087561	K562	blood:	n/a	n/a
19	POLR2A	chr19:39087156-39087474	GM12878	blood:	n/a	n/a
20	MAX	chr19:39086695-39087660	K562	blood:	n/a	chr19:39087537-39087547 chr19:39086919-39086929
21	CCNT2	chr19:39086842-39087596	K562	blood:	n/a	n/a
22	MAX	chr19:39086726-39087740	ECC-1	luminal epithelium:	n/a	chr19:39087537-39087547 chr19:39086919-39086929
23	JUN	chr19:39086593-39087928	K562	blood:	n/a	chr19:39087791-39087802
24	ZNF143	chr19:39086792-39087438	H1-hESC	embryonic stem cell:	n/a	n/a
25	SP4	chr19:39086733-39087433	H1-hESC	embryonic stem cell:	n/a	chr19:39086880-39086896 chr19:39086916-39086932 chr19:39087143-39087154 chr19:39087178-39087194 chr19:39086758-39086774 chr19:39087176-39087192 chr19:39087303-39087319
26	MAX	chr19:39086704-39087774	HCT-116	colon:	n/a	chr19:39087537-39087547 chr19:39086919-39086929
27	MXI1	chr19:39086875-39087434	H1-hESC	embryonic stem cell:	n/a	n/a
28	TCF12	chr19:39086752-39087445	ECC-1	luminal epithelium:	n/a	n/a
29	RCOR1	chr19:39086728-39087474	K562	blood:	n/a	n/a
30	TCF12	chr19:39087330-39087544	H1-hESC	embryonic stem cell:	n/a	chr19:39087466-39087473
31	SP1	chr19:39086584-39087687	A549	lung:	n/a	chr19:39086670-39086680 chr19:39086894-39086906 chr19:39086761-39086770 chr19:39086919-39086928 chr19:39087558-39087568 chr19:39087558-39087567 chr19:39086884-39086893 chr19:39087180-39087192 chr19:39086894-39086906 chr19:39086882-39086894 chr19:39086919-39086929 chr19:39086920-39086929 chr19:39086760-39086772 chr19:39087538-39087547 chr19:39087536-39087548 chr19:39087181-39087191 chr19:39087143-39087154 chr19:39087306-39087316 chr19:39086762-39086771 chr19:39086883-39086897 chr19:39087557-39087569 chr19:39087537-39087547 chr19:39087306-39087316 chr19:39086761-39086771 chr19:39087145-39087154 chr19:39087536-39087548 chr19:39086918-39086930 chr19:39087537-39087546 chr19:39087559-39087568 chr19:39086761-39086771 chr19:39086760-39086772 chr19:39086895-39086904 chr19:39086761-39086770 chr19:39086918-39086930 chr19:39087559-39087568 chr19:39086649-39086659 chr19:39087557-39087569 chr19:39086919-39086933 chr19:39087537-39087547 chr19:39087181-39087191 chr19:39087180-39087192 chr19:39087533-39087547 chr19:39086883-39086892
32	GABPA	chr19:39086883-39087391	K562	blood:	n/a	n/a
33	SP1	chr19:39086660-39087590	A549	lung:	n/a	chr19:39086670-39086680 chr19:39086894-39086906 chr19:39086761-39086770 chr19:39086919-39086928 chr19:39087558-39087568 chr19:39087558-39087567 chr19:39086884-39086893 chr19:39087180-39087192 chr19:39086894-39086906 chr19:39086882-39086894 chr19:39086919-39086929 chr19:39086920-39086929 chr19:39086760-39086772 chr19:39087538-39087547 chr19:39087536-39087548 chr19:39087181-39087191 chr19:39087143-39087154 chr19:39087306-39087316 chr19:39086762-39086771 chr19:39086883-39086897 chr19:39087557-39087569 chr19:39087537-39087547 chr19:39087306-39087316 chr19:39086761-39086771 chr19:39087145-39087154 chr19:39087536-39087548 chr19:39086918-39086930 chr19:39087537-39087546 chr19:39087559-39087568 chr19:39086761-39086771 chr19:39086760-39086772 chr19:39086895-39086904 chr19:39086761-39086770 chr19:39086918-39086930 chr19:39087559-39087568 chr19:39087557-39087569 chr19:39086919-39086933 chr19:39087537-39087547 chr19:39087181-39087191 chr19:39087180-39087192 chr19:39087533-39087547 chr19:39086883-39086892
34	HCFC1	chr19:39087276-39087408	K562	blood:	n/a	n/a
35	MAZ	chr19:39086757-39087941	K562	blood:	n/a	chr19:39087537-39087547 chr19:39086919-39086929 chr19:39087925-39087935
36	BCL3	chr19:39086794-39087535	A549	lung:	n/a	chr19:39087476-39087485 chr19:39086895-39086904 chr19:39086912-39086919
37	IRF1	chr19:39086692-39087926	K562	blood:	n/a	chr19:39086880-39086894 chr19:39086758-39086772 chr19:39086892-39086906 chr19:39087557-39087571 chr19:39086916-39086930 chr19:39087180-39087194 chr19:39087536-39087550
38	SP1	chr19:39086670-39087556	H1-hESC	embryonic stem cell:	n/a	chr19:39086670-39086680 chr19:39086894-39086906 chr19:39086761-39086770 chr19:39086919-39086928 chr19:39086884-39086893 chr19:39087180-39087192 chr19:39086894-39086906 chr19:39086882-39086894 chr19:39086919-39086929 chr19:39086920-39086929 chr19:39086760-39086772 chr19:39087538-39087547 chr19:39087536-39087548 chr19:39087181-39087191 chr19:39087143-39087154 chr19:39087306-39087316 chr19:39086762-39086771 chr19:39086883-39086897 chr19:39087537-39087547 chr19:39087306-39087316 chr19:39086761-39086771 chr19:39087145-39087154 chr19:39087536-39087548 chr19:39086918-39086930 chr19:39087537-39087546 chr19:39086761-39086771 chr19:39086760-39086772 chr19:39086895-39086904 chr19:39086761-39086770 chr19:39086918-39086930 chr19:39086919-39086933 chr19:39087537-39087547 chr19:39087181-39087191 chr19:39087180-39087192 chr19:39087533-39087547 chr19:39086883-39086892
39	MAX	chr19:39086672-39087756	HCT-116	colon:	n/a	chr19:39087537-39087547 chr19:39086919-39086929
40	E2F6	chr19:39086816-39087408	K562	blood:	n/a	chr19:39086884-39086893 chr19:39087339-39087354 chr19:39087080-39087095
41	RAD21	chr19:39087330-39087558	K562	blood:	n/a	n/a
42	POLR2A	chr19:39086846-39087999	GM12878	blood:	n/a	n/a
43	E2F6	chr19:39086867-39087585	A549	lung:	n/a	chr19:39086884-39086893 chr19:39087339-39087354 chr19:39087080-39087095
44	CTCF	chr19:39087333-39087534	K562	blood:	n/a	n/a
45	SP1	chr19:39086598-39087735	H1-hESC	embryonic stem cell:	n/a	chr19:39086670-39086680 chr19:39086894-39086906 chr19:39086761-39086770 chr19:39086919-39086928 chr19:39087558-39087568 chr19:39087558-39087567 chr19:39086884-39086893 chr19:39087180-39087192 chr19:39086894-39086906 chr19:39086882-39086894 chr19:39086919-39086929 chr19:39086920-39086929 chr19:39086760-39086772 chr19:39087538-39087547 chr19:39087536-39087548 chr19:39087181-39087191 chr19:39087143-39087154 chr19:39087306-39087316 chr19:39086762-39086771 chr19:39086883-39086897 chr19:39087557-39087569 chr19:39087537-39087547 chr19:39087306-39087316 chr19:39086761-39086771 chr19:39087145-39087154 chr19:39087536-39087548 chr19:39086918-39086930 chr19:39087537-39087546 chr19:39087559-39087568 chr19:39086761-39086771 chr19:39086760-39086772 chr19:39086895-39086904 chr19:39086761-39086770 chr19:39086918-39086930 chr19:39087559-39087568 chr19:39086649-39086659 chr19:39087557-39087569 chr19:39086919-39086933 chr19:39087537-39087547 chr19:39087181-39087191 chr19:39087180-39087192 chr19:39087533-39087547 chr19:39086883-39086892
46	E2F6	chr19:39086864-39087566	K562	blood:	n/a	chr19:39086884-39086893 chr19:39087339-39087354 chr19:39087080-39087095
47	MAX	chr19:39087001-39087499	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3A	chr19:39086726-39087643	H1-hESC	embryonic stem cell:	n/a	chr19:39087342-39087353
49	TCF12	chr19:39086819-39087663	A549	lung:	n/a	chr19:39087466-39087473
50	MAX	chr19:39086740-39087738	ECC-1	luminal epithelium:	n/a	chr19:39087537-39087547 chr19:39086919-39086929

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39086053..39087682-chr19:39099165..39101048,2	K562	blood:
2	chr19:39086098..39088583-chr19:39106611..39110096,5	K562	blood:

Variant related genes	Relation type
MAP4K1	TF binding region
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10404936	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10408694	0.89[ASN][1000 genomes]
rs10408718	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10413936	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13345914	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17847678	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1978444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2080987	0.80[AFR][1000 genomes]
rs2098657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2287731	0.80[AMR][1000 genomes]
rs2287734	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2287735	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2303041	0.82[EUR][1000 genomes]
rs2368477	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4802618	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922338	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59727665	0.86[EUR][1000 genomes]
rs73552634	0.80[AMR][1000 genomes]
rs750437	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking 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	37 gene(s)	inside rSNPs	diseases
6	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription 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 target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39070600-39100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:39074800-39101600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr19:39076600-39089600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:39076600-39093200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:39076800-39092800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr19:39077000-39101600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:39077200-39103200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr19:39077800-39093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:39078000-39088400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:39078000-39089000	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr19:39078000-39089200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:39078000-39089800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:39078200-39092200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:39081000-39088600	Strong transcription	Thymus	Thymus
15	chr19:39081400-39088400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:39082600-39088600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:39083400-39088600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:39083600-39088600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:39083800-39088600	Strong transcription	GM12878-XiMat	blood
20	chr19:39085000-39088600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr19:39086000-39088400	Strong transcription	Dnd41	blood
22	chr19:39086200-39088400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:39086200-39088600	Strong transcription	Primary B cells from cord blood	blood
24	chr19:39086400-39087400	Genic enhancers	Spleen	Spleen
25	chr19:39086400-39087600	Enhancers	Esophagus	oesophagus
26	chr19:39086400-39087800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr19:39086400-39087800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr19:39086400-39087800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr19:39086400-39096600	Weak transcription	Fetal Thymus	thymus
30	chr19:39086400-39098400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:39086600-39087400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:39086600-39087400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:39086600-39087400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:39086600-39087400	Active TSS	K562	blood
35	chr19:39086600-39087600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr19:39086600-39087600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr19:39086600-39087600	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr19:39086600-39087800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr19:39086600-39088000	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr19:39086600-39088000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr19:39086600-39088000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:39086800-39087400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:39086800-39087400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:39086800-39087400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr19:39086800-39087400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr19:39086800-39087400	Bivalent Enhancer	Fetal Stomach	stomach
47	chr19:39086800-39087400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr19:39086800-39087400	Active TSS	Hela-S3	cervix
49	chr19:39086800-39087600	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr19:39086800-39087600	Enhancers	Skeletal Muscle Male	skeletal muscle

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