Variant report

Variant	rs16857959
Chromosome Location	chr2:12005719-12005720
allele	C/T
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	BATF	chr2:12005399-12005774	GM12878	blood:	n/a	n/a
2	EGR1	chr2:12005550-12005761	GM12878	blood:	n/a	chr2:12005624-12005638
3	NFIC	chr2:12005366-12005877	GM12878	blood:	n/a	n/a
4	EP300	chr2:12005491-12005901	GM12878	blood:	n/a	n/a
5	MTA3	chr2:12005364-12005903	GM12878	blood:	n/a	n/a
6	EBF1	chr2:12005409-12005898	GM12878	blood:	n/a	chr2:12005661-12005672
7	TCF3	chr2:12005523-12005774	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr2:12005530-12005902	GM12878	blood:	n/a	n/a
9	RELA	chr2:12005473-12005976	GM18505	blood:	n/a	n/a
10	ATF2	chr2:12005434-12005910	GM12878	blood:	n/a	n/a
11	SPI1	chr2:12005578-12006043	GM12891	blood:	n/a	n/a
12	ATF2	chr2:12005451-12005784	GM12878	blood:	n/a	n/a
13	STAT1	chr2:12005577-12005744	GM12878	blood:	n/a	n/a
14	SP1	chr2:12005436-12005838	GM12878	blood:	n/a	n/a
15	CUX1	chr2:12005540-12005831	GM12878	blood:	n/a	n/a
16	BHLHE40	chr2:12005423-12006000	GM12878	blood:	n/a	n/a
17	NFIC	chr2:12005355-12005873	GM12878	blood:	n/a	n/a
18	PAX5	chr2:12005425-12005747	GM12878	blood:	n/a	n/a
19	EBF1	chr2:12005520-12005815	GM12878	blood:	n/a	chr2:12005661-12005672
20	PAX5	chr2:12005468-12005774	GM12878	blood:	n/a	n/a
21	EBF1	chr2:12005443-12005947	GM12878	blood:	n/a	chr2:12005661-12005672
22	EGR1	chr2:12005534-12005722	GM12878	blood:	n/a	chr2:12005624-12005638
23	ZNF143	chr2:12005586-12005879	GM12878	blood:	n/a	n/a
24	RUNX3	chr2:12005450-12005841	GM12878	blood:	n/a	n/a
25	TCF12	chr2:12005512-12005786	GM12878	blood:	n/a	n/a
26	EP300	chr2:12005480-12005824	GM12878	blood:	n/a	n/a
27	SPI1	chr2:12005500-12005974	GM12878	blood:	n/a	n/a
28	BATF	chr2:12005424-12005818	GM12878	blood:	n/a	n/a
29	ELF1	chr2:12005482-12005897	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LPIN1-1	chr2:12005638-12005889	NONHSAT069206

Variant related genes	Relation type
ENSG00000224184	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16857985	0.81[AFR][1000 genomes]
rs2577268	0.94[EUR][1000 genomes]
rs2716622	0.94[EUR][1000 genomes]
rs2716623	0.94[EUR][1000 genomes]
rs2716633	0.94[EUR][1000 genomes]
rs4387758	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv833403	chr2:11944552-12125634	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
5	nsv508710	chr2:11982971-12028555	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12000200-12007800	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:12002400-12006800	Enhancers	Primary B cells from cord blood	blood
3	chr2:12003200-12009600	Weak transcription	Right Atrium	heart
4	chr2:12003400-12005800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:12004200-12007000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:12004200-12012600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:12004400-12005800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:12004400-12005800	Enhancers	GM12878-XiMat	blood
9	chr2:12004400-12008200	Weak transcription	NHEK	skin
10	chr2:12004400-12012600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:12004400-12012800	Weak transcription	Esophagus	oesophagus
12	chr2:12004400-12012800	Weak transcription	Stomach Mucosa	stomach
13	chr2:12004400-12015400	Weak transcription	Gastric	stomach
14	chr2:12004600-12006000	Weak transcription	Left Ventricle	heart
15	chr2:12004600-12006000	Weak transcription	Lung	lung
16	chr2:12004600-12006200	Weak transcription	K562	blood
17	chr2:12004600-12006600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:12004600-12008000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:12004600-12008200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:12004600-12009600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:12004600-12010000	Weak transcription	Fetal Heart	heart
22	chr2:12004600-12012800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:12004800-12006000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:12004800-12006000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:12004800-12006400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:12004800-12007800	Weak transcription	HMEC	breast
27	chr2:12004800-12009200	Weak transcription	NH-A	brain
28	chr2:12004800-12010000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:12005000-12006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:12005000-12006000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:12005000-12006200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:12005000-12009600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:12005000-12009600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:12005000-12013600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:12005400-12005800	Weak transcription	Spleen	Spleen
36	chr2:12005600-12006200	Bivalent Enhancer	Placenta	Placenta

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