Variant report

Variant	rs41446950
Chromosome Location	chr19:43033156-43033157
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	RAD21	chr19:43033147-43034049	HCT-116	colon:	n/a	chr19:43033583-43033602 chr19:43033676-43033686
2	HEY1	chr19:43032316-43033163	HepG2	liver:	n/a	n/a
3	RAD21	chr19:43033139-43034045	A549	lung:	n/a	chr19:43033583-43033602 chr19:43033676-43033686
4	ELF1	chr19:43032363-43033854	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:43032930-43033678	HepG2	liver:	n/a	n/a
6	NFIC	chr19:43033075-43033760	HepG2	liver:	n/a	n/a
7	CTCF	chr19:43033140-43033290	GM12873	blood:	n/a	n/a
8	CTCF	chr19:43031752-43034268	A549	lung:	n/a	chr19:43033585-43033603 chr19:43033591-43033600
9	POLR2A	chr19:43032389-43033651	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:43032363-43033285	HepG2	liver:	n/a	n/a
11	CHD2	chr19:43032516-43033740	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:43032313-43033658	GM12891	blood:	n/a	n/a
13	CTCF	chr19:43033060-43033210	HCFaa	heart:	n/a	n/a
14	SMC3	chr19:43032420-43033878	GM12878	blood:	n/a	chr19:43032528-43032542
15	CTCF	chr19:43033120-43033270	BJ	skin:	n/a	n/a
16	CTCF	chr19:43033080-43033230	HEEpiC	esophagus:	n/a	n/a
17	POLR2A	chr19:43032318-43033643	HepG2	liver:	n/a	n/a
18	ZBTB7A	chr19:43033046-43033218	HepG2	liver:	n/a	n/a
19	RUNX3	chr19:43033152-43033808	GM12878	blood:	n/a	n/a
20	TCF12	chr19:43033093-43034018	A549	lung:	n/a	chr19:43033361-43033368
21	CTCF	chr19:43033100-43033250	HFF	foreskin:	n/a	n/a
22	POLR2A	chr19:43032168-43033560	HepG2	liver:	n/a	n/a
23	CTCF	chr19:43033068-43034263	SK-N-SH	brain:	n/a	chr19:43033585-43033603 chr19:43033591-43033600

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42954301..42955305-chr19:43033122..43034033,12	MCF-7	breast:
2	chr19:42954315..42955211-chr19:43033063..43034067,7	K562	blood:

Variant related genes	Relation type
CEACAM1	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16975752	1.00[AMR][1000 genomes]
rs16975764	1.00[AMR][1000 genomes]
rs16980938	1.00[AMR][1000 genomes]
rs41370146	1.00[AMR][1000 genomes]
rs41399845	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41454446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs45517531	1.00[AMR][1000 genomes]
rs45542933	1.00[AMR][1000 genomes]
rs45600939	1.00[AMR][1000 genomes]
rs8110553	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2422468	chr19:42991289-43669027	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1057390	chr19:43003323-43173028	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43023600-43033200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:43030400-43033400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
3	chr19:43030400-43033600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr19:43030400-43033600	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:43031000-43033600	Enhancers	Spleen	Spleen
6	chr19:43031200-43033600	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr19:43031400-43033600	Flanking Active TSS	Liver	Liver
8	chr19:43031600-43033600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:43031600-43033600	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr19:43031600-43033600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr19:43031800-43033600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr19:43032000-43033400	Enhancers	Brain Cingulate Gyrus	brain
13	chr19:43032000-43033400	Enhancers	A549	lung
14	chr19:43032000-43033600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr19:43032000-43033600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr19:43032000-43033600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:43032000-43033600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr19:43032000-43033600	Enhancers	Fetal Muscle Leg	muscle
19	chr19:43032000-43033600	Enhancers	Gastric	stomach
20	chr19:43032000-43033800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr19:43032200-43033200	Active TSS	Small Intestine	intestine
22	chr19:43032200-43033400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:43032200-43033400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr19:43032200-43033600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:43032200-43033600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:43032200-43033600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:43032200-43033600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:43032200-43033600	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr19:43032200-43033600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr19:43032200-43033600	Flanking Active TSS	GM12878-XiMat	blood
31	chr19:43032200-43033800	Enhancers	Lung	lung
32	chr19:43032400-43033200	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr19:43032400-43033200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:43032400-43033200	Active TSS	HepG2	liver
35	chr19:43032400-43033200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr19:43032400-43033200	Flanking Active TSS	NHEK	skin
37	chr19:43032400-43033400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:43032400-43033400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr19:43032400-43033400	Enhancers	Pancreas	Pancrea
40	chr19:43032400-43033400	Enhancers	Thymus	Thymus
41	chr19:43032400-43033400	Flanking Active TSS	Dnd41	blood
42	chr19:43032400-43033400	Flanking Active TSS	HMEC	breast
43	chr19:43032400-43033600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:43032400-43033600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr19:43032400-43033600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:43032400-43033600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr19:43032400-43033600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:43032400-43033600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:43032400-43033600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr19:43032400-43033600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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