Variant report

Variant	rs6855875
Chromosome Location	chr4:148402737-148402738
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	MAX	chr4:148402002-148403028	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr4:148402318-148402969	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr4:148402043-148403172	ECC-1	luminal epithelium:	n/a	chr4:148403159-148403168
4	ZNF263	chr4:148400958-148403107	HEK293-T-REx	kidney:	n/a	n/a
5	TCF7L2	chr4:148401913-148403011	HCT-116	colon:	n/a	n/a
6	E2F6	chr4:148402050-148403058	H1-hESC	embryonic stem cell:	n/a	chr4:148402480-148402490 chr4:148402070-148402080 chr4:148402403-148402413
7	POLR2A	chr4:148401781-148403382	SK-N-MC	brain:	n/a	n/a
8	MXI1	chr4:148400942-148403441	IMR90	lung:	n/a	n/a
9	ZBTB7A	chr4:148402162-148402919	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr4:148402335-148403246	H1-hESC	embryonic stem cell:	n/a	chr4:148403159-148403168
11	SIN3A	chr4:148401853-148403134	H1-hESC	embryonic stem cell:	n/a	chr4:148402645-148402656
12	TBP	chr4:148401957-148403105	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr4:148402492-148403165	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr4:148401876-148403188	IMR90	lung:	n/a	n/a
15	RAD21	chr4:148401977-148403023	IMR90	lung:	n/a	chr4:148402900-148402909 chr4:148402671-148402685 chr4:148402465-148402479
16	ZBTB7A	chr4:148402210-148402839	ECC-1	luminal epithelium:	n/a	n/a
17	TAF1	chr4:148401919-148403178	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148398530..148400390-chr4:148402721..148404279,2	MCF-7	breast:
2	chr4:148400285..148404582-chr4:148404756..148408817,4	K562	blood:

Variant related genes	Relation type
EDNRA	TF binding region
ENSG00000151617	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10011966	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10024834	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10305860	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10305862	0.96[ASN][1000 genomes]
rs11100963	0.84[ASN][1000 genomes]
rs11722942	0.85[ASN][1000 genomes]
rs11727337	0.85[ASN][1000 genomes]
rs11727397	0.85[ASN][1000 genomes]
rs11730985	0.85[ASN][1000 genomes]
rs11731096	0.81[ASN][1000 genomes]
rs11731097	0.81[ASN][1000 genomes]
rs11731134	0.85[ASN][1000 genomes]
rs12509416	0.86[ASN][1000 genomes]
rs12642328	0.86[ASN][1000 genomes]
rs13112065	0.85[ASN][1000 genomes]
rs13127894	0.83[ASN][1000 genomes]
rs13143677	0.89[ASN][1000 genomes]
rs13144507	0.87[ASN][1000 genomes]
rs1366688	0.82[ASN][1000 genomes]
rs1400554	0.83[ASN][1000 genomes]
rs1400558	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs1400559	0.85[ASN][1000 genomes]
rs1400560	0.85[ASN][1000 genomes]
rs1517134	0.93[ASN][1000 genomes]
rs1517138	0.85[ASN][1000 genomes]
rs1517139	0.85[ASN][1000 genomes]
rs17474816	0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17474823	0.81[ASN][1000 genomes]
rs1801708	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1949375	0.85[ASN][1000 genomes]
rs1996373	0.93[ASN][1000 genomes]
rs1996374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2063936	0.85[ASN][1000 genomes]
rs34256803	0.84[ASN][1000 genomes]
rs35686091	0.84[ASN][1000 genomes]
rs4631019	0.83[ASN][1000 genomes]
rs4835081	0.85[ASN][1000 genomes]
rs4835083	0.96[ASN][1000 genomes]
rs4835084	0.96[ASN][1000 genomes]
rs4835086	0.81[ASN][1000 genomes]
rs4835401	0.85[ASN][1000 genomes]
rs4835405	0.85[ASN][1000 genomes]
rs4835407	0.85[ASN][1000 genomes]
rs4835410	0.96[ASN][1000 genomes]
rs56015601	0.96[ASN][1000 genomes]
rs57886575	0.81[ASN][1000 genomes]
rs6537479	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs6537480	0.95[ASN][1000 genomes]
rs6537483	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6537484	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6817469	0.83[ASN][1000 genomes]
rs6819740	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6820938	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6823537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6840108	0.82[ASN][1000 genomes]
rs6840756	0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6840784	0.83[ASN][1000 genomes]
rs6848108	0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6853791	0.81[ASN][1000 genomes]
rs702757	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7655670	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7659823	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7663891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9308218	0.96[ASN][1000 genomes]
rs952402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs959600	0.85[ASN][1000 genomes]
rs984457	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs984458	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9991584	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830109	chr4:148295061-148468605	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6855875	DCLK2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148401200-148404000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
2	chr4:148401400-148404400	Active TSS	Right Ventricle	heart
3	chr4:148401400-148404600	Active TSS	Fetal Kidney	kidney
4	chr4:148401600-148402800	Active TSS	Rectal Smooth Muscle	rectum
5	chr4:148401600-148403000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:148401600-148403200	Active TSS	Duodenum Mucosa	Duodenum
7	chr4:148401600-148403600	Active TSS	Fetal Lung	lung
8	chr4:148401800-148402800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:148401800-148402800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr4:148401800-148402800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
11	chr4:148401800-148402800	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:148401800-148402800	Active TSS	NHLF	lung
13	chr4:148401800-148403000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:148401800-148403000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr4:148401800-148403000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr4:148401800-148403000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
17	chr4:148401800-148403200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr4:148401800-148403200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:148401800-148403200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:148401800-148403200	Active TSS	Aorta	Aorta
21	chr4:148401800-148403200	Active TSS	Lung	lung
22	chr4:148401800-148403400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:148401800-148404000	Bivalent/Poised TSS	Fetal Thymus	thymus
24	chr4:148401800-148404200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:148401800-148404200	Active TSS	Left Ventricle	heart
26	chr4:148401800-148404400	Active TSS	Ovary	ovary
27	chr4:148401800-148404600	Active TSS	Right Atrium	heart
28	chr4:148402000-148402800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:148402000-148402800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:148402000-148402800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:148402000-148402800	Active TSS	Brain Substantia Nigra	brain
32	chr4:148402000-148402800	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr4:148402000-148402800	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr4:148402000-148402800	Active TSS	NHDF-Ad	bronchial
35	chr4:148402000-148403000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr4:148402000-148403000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:148402000-148403000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:148402000-148403000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:148402000-148403000	Active TSS	Brain Anterior Caudate	brain
40	chr4:148402000-148403000	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr4:148402000-148403000	Active TSS	Colonic Mucosa	Colon
42	chr4:148402000-148403000	Active TSS	Colon Smooth Muscle	Colon
43	chr4:148402000-148403000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:148402000-148403000	Bivalent/Poised TSS	Fetal Stomach	stomach
45	chr4:148402000-148403000	ZNF genes & repeats	Spleen	Spleen
46	chr4:148402000-148403200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr4:148402000-148403200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:148402000-148403200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr4:148402000-148403200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr4:148402000-148403200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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