Variant report

Variant	rs12461670
Chromosome Location	chr19:44284315-44284316
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	MAX	chr19:44283305-44284355	NB4	blood:	n/a	n/a
2	CTCF	chr19:44284180-44284330	GM12866	blood:	n/a	chr19:44284213-44284226
3	POLR2A	chr19:44284249-44284442	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr19:44284180-44284330	GM12869	blood:	n/a	chr19:44284213-44284226
5	CTCF	chr19:44283519-44285246	A549	lung:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
6	JUND	chr19:44284017-44284379	K562	blood:	n/a	n/a
7	SMC3	chr19:44284033-44284433	GM12878	blood:	n/a	n/a
8	CTCF	chr19:44283994-44284453	GM12878	blood:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
9	CTCF	chr19:44284180-44284330	HRE	kidney:	n/a	chr19:44284213-44284226
10	POLR2A	chr19:44280377-44284435	GM12878	blood:	n/a	n/a
11	BCLAF1	chr19:44283903-44284461	GM12878	blood:	n/a	n/a
12	CTCF	chr19:44284180-44284330	HCT-116	colon:	n/a	chr19:44284213-44284226
13	CTCF	chr19:44283974-44284453	K562	blood:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
14	POLR2A	chr19:44284001-44284350	GM12878	blood:	n/a	n/a
15	BCLAF1	chr19:44283702-44284374	GM12878	blood:	n/a	n/a
16	ZNF263	chr19:44284130-44285070	K562	blood:	n/a	chr19:44284533-44284554 chr19:44284496-44284517
17	CTCF	chr19:44284114-44284341	H1-hESC	embryonic stem cell:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
18	FOXA2	chr19:44283919-44284568	A549	lung:	n/a	n/a
19	CTCF	chr19:44284220-44284370	HBMEC	blood vessel:	n/a	chr19:44284329-44284338
20	POLR2A	chr19:44282657-44284379	HL-60	blood:	n/a	n/a
21	NFIC	chr19:44283786-44284415	GM12878	blood:	n/a	n/a
22	RCOR1	chr19:44282814-44284372	K562	blood:	n/a	n/a
23	TEAD4	chr19:44283888-44284400	K562	blood:	n/a	n/a
24	EBF1	chr19:44284040-44284592	GM12878	blood:	n/a	chr19:44284327-44284338
25	CTCF	chr19:44284300-44284450	HL-60	blood:	n/a	chr19:44284329-44284338
26	POLR2A	chr19:44283214-44284391	HL-60	blood:	n/a	n/a
27	WRNIP1	chr19:44282851-44284495	GM12878	blood:	n/a	n/a
28	CTCF	chr19:44284180-44284330	MCF-7	breast:	n/a	chr19:44284213-44284226
29	CTCF	chr19:44284114-44284339	GM19239	blood:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
30	ZNF384	chr19:44283957-44284368	GM12878	blood:	n/a	n/a
31	ZBTB7A	chr19:44284021-44284547	K562	blood:	n/a	n/a
32	CTCF	chr19:44284200-44284350	AG10803	skin:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
33	CBX3	chr19:44284025-44284407	K562	blood:	n/a	n/a
34	TCF12	chr19:44283560-44284513	A549	lung:	n/a	n/a
35	POLR2A	chr19:44282699-44284463	GM18505	blood:	n/a	n/a
36	CHD2	chr19:44283979-44284359	K562	blood:	n/a	n/a
37	CHD2	chr19:44282867-44284408	GM12878	blood:	n/a	n/a
38	CUX1	chr19:44283880-44284417	K562	blood:	n/a	n/a
39	NR2F2	chr19:44283564-44284425	MCF-7	breast:	n/a	n/a
40	PML	chr19:44282967-44284488	GM12878	blood:	n/a	n/a
41	CTCF	chr19:44284200-44284350	HUVEC	blood vessel:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
42	RUNX3	chr19:44283705-44284371	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:44282671-44284425	GM12891	blood:	n/a	n/a
44	POLR2A	chr19:44284041-44284353	K562	blood:	n/a	n/a
45	CTCF	chr19:44284073-44284369	GM19238	blood:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
46	POLR2A	chr19:44283508-44284586	HCT-116	colon:	n/a	n/a
47	POLR2A	chr19:44282566-44285595	GM12878	blood:	n/a	n/a
48	CTCF	chr19:44284189-44284332	GM12891	blood:	n/a	chr19:44284213-44284226
49	TBL1XR1	chr19:44284097-44284366	K562	blood:	n/a	n/a
50	RAD21	chr19:44284076-44284367	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44258057..44261358-chr19:44282388..44285287,3	MCF-7	breast:
2	chr19:44269561..44270470-chr19:44283736..44284661,2	MCF-7	breast:
3	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
4	chr19:44270615..44271921-chr19:44283761..44284756,6	MCF-7	breast:
5	chr19:44256077..44259725-chr19:44281509..44284317,6	MCF-7	breast:

Variant related genes	Relation type
KCNN4	TF binding region
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11666781	0.85[ASN][1000 genomes]
rs11673595	0.84[ASN][1000 genomes]
rs11673603	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34257765	0.85[ASN][1000 genomes]
rs379758	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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 target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44280800-44284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44280800-44285800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:44281000-44284600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr19:44281200-44284400	Enhancers	HUVEC	blood vessel
5	chr19:44281200-44285600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:44281400-44287000	Enhancers	Spleen	Spleen
7	chr19:44281800-44284400	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr19:44281800-44285400	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:44281800-44285600	Enhancers	Fetal Intestine Large	intestine
10	chr19:44282000-44285600	Enhancers	Lung	lung
11	chr19:44282200-44284800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:44282200-44286800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:44282400-44284800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:44282400-44285000	Weak transcription	NHDF-Ad	bronchial
15	chr19:44282400-44289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:44282600-44284400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:44282600-44284400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr19:44282600-44284400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:44282600-44284600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:44282800-44284400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr19:44282800-44284400	Flanking Active TSS	Thymus	Thymus
22	chr19:44282800-44284400	Flanking Active TSS	K562	blood
23	chr19:44282800-44284600	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr19:44282800-44284600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:44282800-44285800	Flanking Active TSS	Placenta	Placenta
26	chr19:44283000-44284400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:44283000-44284400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr19:44283000-44284600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr19:44283000-44284600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:44283000-44284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:44283000-44285000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:44283000-44285200	Flanking Active TSS	Colonic Mucosa	Colon
33	chr19:44283000-44285400	Flanking Active TSS	Fetal Thymus	thymus
34	chr19:44283000-44286000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:44283200-44284400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:44283200-44284600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr19:44283200-44284600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr19:44283200-44285000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr19:44283200-44285600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:44283400-44284800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:44283400-44284800	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:44283400-44284800	Enhancers	Fetal Intestine Small	intestine
43	chr19:44283400-44284800	Weak transcription	Fetal Muscle Leg	muscle
44	chr19:44283400-44285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:44283400-44285200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:44283400-44285200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr19:44283600-44284400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr19:44283600-44284400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr19:44283600-44284400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr19:44283600-44284400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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