Variant report

Variant	rs2688247
Chromosome Location	chr4:8442002-8442003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:185)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:185 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr4:8441904-8442700	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr4:8441939-8442723	U87	brain:	n/a	n/a
3	POLR2A	chr4:8441878-8442778	GM18505	blood:	n/a	n/a
4	JUN	chr4:8440970-8443464	K562	blood:	n/a	chr4:8442293-8442304 chr4:8442412-8442426
5	TBL1XR1	chr4:8441937-8442693	K562	blood:	n/a	n/a
6	MXI1	chr4:8440826-8443653	IMR90	lung:	n/a	n/a
7	TCF7L2	chr4:8441984-8442568	Hela-S3	cervix:	n/a	n/a
8	SETDB1	chr4:8441778-8442651	K562	blood:	n/a	n/a
9	MYC	chr4:8441673-8443292	NB4	blood:	n/a	n/a
10	POLR2A	chr4:8441942-8442020	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:8441767-8442937	PFSK-1	brain:	n/a	n/a
12	MAX	chr4:8441561-8442699	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr4:8441947-8442804	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr4:8441580-8442713	Hela-S3	cervix:	n/a	n/a
15	TBP	chr4:8441926-8442752	K562	blood:	n/a	n/a
16	YY1	chr4:8441966-8442726	GM12892	blood:	n/a	n/a
17	TAL1	chr4:8441567-8442666	K562	blood:	n/a	n/a
18	POLR2A	chr4:8441701-8442721	GM12892	blood:	n/a	n/a
19	CREB1	chr4:8441921-8443230	HepG2	liver:	n/a	chr4:8442471-8442484
20	MYC	chr4:8441580-8442686	K562	blood:	n/a	n/a
21	WRNIP1	chr4:8441919-8442631	GM12878	blood:	n/a	n/a
22	EP300	chr4:8441940-8442580	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:8440524-8443902	MCF10A-Er-Src	breast:	n/a	n/a
24	CEBPB	chr4:8441617-8442485	K562	blood:	n/a	n/a
25	KAP1	chr4:8441828-8442580	U2OS	brain:	n/a	n/a
26	MTA3	chr4:8441899-8442755	GM12878	blood:	n/a	n/a
27	MYC	chr4:8441369-8442765	K562	blood:	n/a	n/a
28	EBF1	chr4:8441877-8442611	GM12878	blood:	n/a	chr4:8442075-8442086
29	POLR2A	chr4:8441861-8442677	K562	blood:	n/a	n/a
30	POLR2A	chr4:8441975-8442723	U87	brain:	n/a	n/a
31	CEBPB	chr4:8441710-8442607	K562	blood:	n/a	n/a
32	TAF1	chr4:8441945-8442810	H1-hESC	embryonic stem cell:	n/a	n/a
33	ATF1	chr4:8441931-8444132	K562	blood:	n/a	n/a
34	POLR2A	chr4:8441853-8442863	U87	brain:	n/a	n/a
35	TBP	chr4:8441681-8442673	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr4:8441982-8442813	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:8441744-8442758	K562	blood:	n/a	n/a
38	TAF1	chr4:8441914-8442736	PFSK-1	brain:	n/a	n/a
39	MAX	chr4:8441927-8442777	GM12878	blood:	n/a	n/a
40	BATF	chr4:8441923-8442164	GM12878	blood:	n/a	n/a
41	BRCA1	chr4:8441992-8442698	Hela-S3	cervix:	n/a	n/a
42	SIN3AK20	chr4:8442000-8442966	HCT-116	colon:	n/a	n/a
43	ZNF143	chr4:8441886-8442698	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr4:8441927-8442950	MCF-7	breast:	n/a	n/a
45	MAFF	chr4:8441785-8442318	K562	blood:	n/a	n/a
46	IRF4	chr4:8441947-8442691	GM12878	blood:	n/a	n/a
47	MAX	chr4:8441899-8442725	NB4	blood:	n/a	n/a
48	EP300	chr4:8441866-8442641	K562	blood:	n/a	n/a
49	JUND	chr4:8441867-8442691	K562	blood:	n/a	chr4:8442293-8442304 chr4:8442412-8442426
50	ATF2	chr4:8441810-8442679	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:8441964-8442014	HRPEpiC	eye:	n/a
2	chr4:8441964-8442014	NHBE	bronchial:	n/a
3	chr4:8441964-8442014	HPAEpiC	pulmonary alveolar:	n/a
4	chr4:8441964-8442014	Caco-2	colon:	n/a
5	chr4:8441964-8442014	ProgFib	skin:	n/a
6	chr4:8441964-8442014	HL-60	blood:	n/a
7	chr4:8441964-8442014	HEEpiC	esophagus:	n/a
8	chr4:8441964-8442014	MCF-7	breast:	n/a
9	chr4:8441964-8442014	HNPCEpiC	eye:	n/a
10	chr4:8441964-8442014	PFSK-1	brain:	n/a
11	chr4:8441964-8442014	U87	brain:	n/a
12	chr4:8441964-8442014	H1-hESC	embryonic stem cell:	embryo
13	chr4:8441964-8442014	BJ	skin:	n/a
14	chr4:8441964-8442014	PANC-1	pancreas:	n/a
15	chr4:8441964-8442014	SKMC	muscle:	n/a
16	chr4:8441964-8442014	HUVEC	blood vessel:	n/a
17	chr4:8441964-8442014	SAEC	small airway:	n/a
18	chr4:8441964-8442014	IMR90	lung:	fetal
19	chr4:8441964-8442014	Hepatocyte	liver:	n/a
20	chr4:8441964-8442014	AG10803	skin:	n/a
21	chr4:8441964-8442014	Jurkat	blood:	n/a
22	chr4:8441964-8442014	GM12878	blood:	n/a
23	chr4:8441964-8442014	NH-A	brain:	n/a
24	chr4:8441964-8442014	MCF10A-Er-Src	breast:	n/a
25	chr4:8441964-8442014	SK-N-SH	brain:	n/a
26	chr4:8441964-8442014	HAEpiC	amniotic membrane:	n/a
27	chr4:8441964-8442014	HCT-116	colon:	n/a
28	chr4:8441964-8442014	AG04450	lung:	fetal
29	chr4:8441964-8442014	AG09319	gingival:	n/a
30	chr4:8441964-8442014	HRE	kidney:	n/a
31	chr4:8441964-8442014	Hela-S3	cervix:	n/a
32	chr4:8441964-8442014	GM12892	blood:	n/a
33	chr4:8441964-8442014	GM12891	blood:	n/a
34	chr4:8441964-8442014	HCPEpiC	choroid plexus:	n/a
35	chr4:8441964-8442014	NB4	blood:	n/a
36	chr4:8441964-8442014	HMEC	breast:	n/a
37	chr4:8441964-8442014	RPTEC	kidney:	n/a
38	chr4:8441964-8442014	AG09309	skin:	n/a
39	chr4:8441964-8442014	A549	lung:	n/a
40	chr4:8441964-8442014	AoSMC	blood vessel:	n/a
41	chr4:8441964-8442014	HEK293	kidney:	embryo
42	chr4:8441964-8442014	LNCaP	prostate:	n/a
43	chr4:8441964-8442014	T-47D	breast:	n/a
44	chr4:8441964-8442014	NT2-D1	testis:	n/a
45	chr4:8441964-8442014	HRCEpiC	kidney:	n/a
46	chr4:8441964-8442014	HIPEpiC	eye:	n/a
47	chr4:8441964-8442014	AG04449	skin:	fetal
48	chr4:8441964-8442014	HCM	heart:	n/a
49	chr4:8441964-8442014	K562	blood:	n/a
50	chr4:8441964-8442014	GM19239	blood:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:8428810..8430394-chr4:8440724..8444143,3	K562	blood:
2	chr4:8439123..8440667-chr4:8441503..8443912,2	K562	blood:
3	chr4:8430205..8432229-chr4:8440824..8442595,2	MCF-7	breast:
4	chr4:8439008..8440667-chr4:8441503..8443852,2	K562	blood:
5	chr4:8428067..8433323-chr4:8440948..8445760,8	K562	blood:

No data

Variant related genes	Relation type
TRMT44	TF binding region
TRMT44	CpG island
ENSG00000155275	Chromatin interaction
ENSG00000087008	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10461079	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1357481	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1543246	0.88[ASN][1000 genomes]
rs1880023	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1880024	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1916326	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1949733	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2010758	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2140337	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2386227	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450475	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2631731	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631734	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631735	0.97[EUR][1000 genomes]
rs2631736	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631740	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2631742	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631743	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631744	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2631745	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631746	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2631754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631756	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2631758	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2631762	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2631768	0.84[EUR][1000 genomes]
rs2688219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688223	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2688224	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688227	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688231	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688233	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2688235	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688242	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2688243	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3103067	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3103069	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103070	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103071	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103072	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3103099	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4696828	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447875	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6837429	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6845969	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6858542	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs868105	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs871768	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs940134	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs940136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2688247	RP11-689P11.2	cis	lung	GTEx
rs2688247	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8439600-8443800	Active TSS	K562	blood
2	chr4:8440800-8443400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:8440800-8443400	Active TSS	Ovary	ovary
4	chr4:8441000-8442200	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr4:8441200-8442200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr4:8441200-8442200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:8441200-8442200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr4:8441200-8442800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:8441400-8442200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:8441400-8442200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr4:8441400-8442200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr4:8441400-8443200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:8441400-8443400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:8441400-8443400	Active TSS	Psoas Muscle	Psoas
15	chr4:8441400-8443400	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr4:8441400-8443400	Active TSS	NHLF	lung
17	chr4:8441400-8443800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:8441400-8444000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr4:8441600-8442200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr4:8441600-8442200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:8441600-8442200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr4:8441600-8442200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr4:8441600-8442200	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr4:8441600-8442200	Flanking Active TSS	Fetal Brain Male	brain
25	chr4:8441600-8442400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr4:8441600-8442600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:8441600-8443000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:8441600-8443000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr4:8441600-8443000	Active TSS	Fetal Brain Female	brain
30	chr4:8441600-8443200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:8441600-8443200	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr4:8441600-8443200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:8441600-8443200	Active TSS	Brain Anterior Caudate	brain
34	chr4:8441600-8443200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:8441600-8443200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr4:8441600-8443400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:8441600-8443400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr4:8441600-8443400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:8441600-8443400	Active TSS	Fetal Kidney	kidney
40	chr4:8441600-8443400	Active TSS	Rectal Smooth Muscle	rectum
41	chr4:8441600-8443400	Active TSS	Right Atrium	heart
42	chr4:8441600-8443400	Active TSS	GM12878-XiMat	blood
43	chr4:8441600-8443400	Active TSS	Hela-S3	cervix
44	chr4:8441600-8443400	Active TSS	HMEC	breast
45	chr4:8441600-8443400	Active TSS	NHDF-Ad	bronchial
46	chr4:8441600-8443400	Active TSS	NHEK	skin
47	chr4:8441600-8443600	Active TSS	Fetal Intestine Small	intestine
48	chr4:8441600-8443800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr4:8441600-8443800	Active TSS	HSMM	muscle
50	chr4:8441600-8445000	Active TSS	HUES64 Cell Line	embryonic stem cell

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