Variant report

Variant	rs10802443
Chromosome Location	chr1:246946856-246946857
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	POLR2A	chr1:246945998-246946892	GM12891	blood:	n/a	n/a
2	NR3C1	chr1:246946178-246946880	A549	lung:	n/a	n/a
3	FOSL2	chr1:246946102-246946919	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:246945912-246946861	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246946643..246948588-chr1:247104112..247106785,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCCPDH-1	chr1:246946701-246947345	NONHSAT010736

Variant related genes	Relation type
KIF28P	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10127783	0.84[ASN][1000 genomes]
rs10159002	0.84[ASN][1000 genomes]
rs10802442	0.84[ASN][1000 genomes]
rs10924820	0.81[ASN][1000 genomes]
rs10924823	0.84[ASN][1000 genomes]
rs10924824	0.84[ASN][1000 genomes]
rs12085330	0.84[ASN][1000 genomes]
rs12090470	0.80[ASN][1000 genomes]
rs12144408	0.83[ASN][1000 genomes]
rs34649985	0.84[ASN][1000 genomes]
rs34989088	0.80[ASN][1000 genomes]
rs3795463	0.84[ASN][1000 genomes]
rs3795464	0.84[ASN][1000 genomes]
rs4244627	0.84[ASN][1000 genomes]
rs4244630	0.83[ASN][1000 genomes]
rs4926454	0.84[ASN][1000 genomes]
rs4926455	0.84[ASN][1000 genomes]
rs4926457	0.84[ASN][1000 genomes]
rs4926459	0.84[ASN][1000 genomes]
rs6664883	0.84[ASN][1000 genomes]
rs6685364	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv3408268	chr1:246944429-246948627	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv1841827	chr1:246944502-246954313	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv3491345	chr1:246945629-246947627	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv3491346	chr1:246945629-246947627	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv1821402	chr1:246945924-246947123	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv15314	chr1:246946311-246946911	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:246932600-246948000	Strong transcription	Liver	Liver
5	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
7	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:246938400-246947200	Strong transcription	Fetal Intestine Small	intestine
11	chr1:246940200-246947600	Weak transcription	HUVEC	blood vessel
12	chr1:246940200-246948800	Weak transcription	Fetal Brain Male	brain
13	chr1:246940400-246949000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:246940600-246948600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:246940600-246948800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:246940600-246948800	Weak transcription	Fetal Kidney	kidney
17	chr1:246940800-246948000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:246940800-246951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:246940800-246951600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:246941200-246948200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:246941200-246952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:246941600-246948800	Weak transcription	Colonic Mucosa	Colon
23	chr1:246941600-246948800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:246941600-246952200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:246942200-246949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:246942800-246952200	Weak transcription	Fetal Brain Female	brain
27	chr1:246943000-246948000	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:246943400-246952000	Weak transcription	Brain Anterior Caudate	brain
29	chr1:246944200-246947800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:246944400-246948800	Weak transcription	Gastric	stomach
31	chr1:246944600-246947800	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr1:246944600-246952200	Weak transcription	NH-A	brain
33	chr1:246944800-246947800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:246944800-246948200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:246944800-246952000	Weak transcription	Fetal Intestine Large	intestine
36	chr1:246944800-246952200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:246945000-246947000	Enhancers	HSMM	muscle
38	chr1:246945000-246948800	Weak transcription	Brain Germinal Matrix	brain
39	chr1:246945200-246948000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:246945200-246949400	Enhancers	Fetal Muscle Leg	muscle
41	chr1:246945600-246947000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:246945600-246947000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:246945800-246947800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:246945800-246948000	Enhancers	Primary T cells from cord blood	blood
45	chr1:246945800-246949000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr1:246945800-246956400	Weak transcription	A549	lung
47	chr1:246946000-246947800	Weak transcription	NHLF	lung
48	chr1:246946000-246948800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:246946200-246947000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:246946200-246947000	Weak transcription	Right Atrium	heart

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