Variant report

Variant	rs34092964
Chromosome Location	chr2:38762893-38762894
allele	C/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	CTCF	chr2:38762760-38762910	GM12873	blood:	n/a	n/a
2	ZNF384	chr2:38762740-38764024	K562	blood:	n/a	n/a
3	RFX5	chr2:38762841-38763515	HepG2	liver:	n/a	n/a
4	CTCF	chr2:38762840-38762990	BJ	skin:	n/a	n/a
5	JUN	chr2:38762762-38763125	HepG2	liver:	n/a	chr2:38762931-38762944 chr2:38762932-38762941
6	MAX	chr2:38762754-38763757	A549	lung:	n/a	chr2:38762773-38762783
7	JUND	chr2:38762753-38763578	K562	blood:	n/a	chr2:38762932-38762941
8	CTCF	chr2:38762860-38763010	HEEpiC	esophagus:	n/a	n/a
9	CTCF	chr2:38762845-38764196	A549	lung:	n/a	chr2:38763399-38763417 chr2:38763400-38763416 chr2:38763402-38763415 chr2:38763404-38763414 chr2:38763402-38763415 chr2:38763399-38763412 chr2:38763402-38763411 chr2:38763401-38763422
10	CTCF	chr2:38762800-38762950	HCPEpiC	choroid plexus:	n/a	n/a
11	ATF2	chr2:38762717-38763443	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr2:38762550-38763854	SK-N-SH	brain:	n/a	chr2:38763399-38763417 chr2:38763400-38763416 chr2:38763402-38763415 chr2:38763404-38763414 chr2:38763402-38763415 chr2:38763399-38763412 chr2:38763402-38763411 chr2:38763401-38763422
13	RAD21	chr2:38762636-38764014	SK-N-SH	brain:	n/a	chr2:38763399-38763413 chr2:38763403-38763416 chr2:38763401-38763410 chr2:38763400-38763419 chr2:38762770-38762780 chr2:38762768-38762780 chr2:38763143-38763156 chr2:38763401-38763415 chr2:38762832-38762845
14	JUND	chr2:38762780-38763547	H1-hESC	embryonic stem cell:	n/a	chr2:38762932-38762941
15	CTCF	chr2:38762840-38762990	GM12872	blood:	n/a	n/a
16	POLR2A	chr2:38761973-38764297	HepG2	liver:	n/a	n/a
17	SMC3	chr2:38762684-38763787	SK-N-SH	brain:	n/a	chr2:38763401-38763415 chr2:38762770-38762780 chr2:38763405-38763415 chr2:38763401-38763408
18	JUND	chr2:38762744-38763132	HepG2	liver:	n/a	chr2:38762932-38762941
19	CTCF	chr2:38762780-38762930	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38762163..38763872-chr2:38974751..38976812,2	K562	blood:
2	chr2:38603492..38605404-chr2:38761964..38764089,2	K562	blood:
3	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
4	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
5	chr2:38602731..38605404-chr2:38761964..38763937,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRPLL-5	chr2:38762710-38762901	NONHSAT070187

Variant related genes	Relation type
ENSG00000271443	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000119787	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10164547	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12105070	0.94[ASN][1000 genomes]
rs12712606	0.81[ASN][1000 genomes]
rs12712608	0.84[ASN][1000 genomes]
rs13030122	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13383838	0.80[ASN][1000 genomes]
rs1579537	0.85[ASN][1000 genomes]
rs17022904	0.86[ASN][1000 genomes]
rs35789272	0.80[EUR][1000 genomes]
rs35803605	0.81[EUR][1000 genomes]
rs3731841	0.93[ASN][1000 genomes]
rs6727476	0.85[ASN][1000 genomes]
rs7571463	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers 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

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38755600-38763000	Weak transcription	Esophagus	oesophagus
2	chr2:38755600-38763000	Weak transcription	Pancreas	Pancrea
3	chr2:38759600-38763000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:38759600-38763000	Weak transcription	Brain Substantia Nigra	brain
5	chr2:38759800-38763000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:38760400-38763000	Enhancers	K562	blood
7	chr2:38760600-38763200	Weak transcription	Aorta	Aorta
8	chr2:38761000-38763800	Active TSS	Colon Smooth Muscle	Colon
9	chr2:38761400-38763000	Enhancers	Brain Anterior Caudate	brain
10	chr2:38761600-38763000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:38761600-38763000	Weak transcription	GM12878-XiMat	blood
12	chr2:38762000-38763000	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr2:38762000-38763400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr2:38762200-38763000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr2:38762200-38763400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr2:38762200-38763800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr2:38762200-38763800	Enhancers	Fetal Brain Male	brain
18	chr2:38762400-38763000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr2:38762400-38763000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:38762400-38763000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr2:38762400-38763000	Bivalent Enhancer	Fetal Stomach	stomach
22	chr2:38762400-38763000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr2:38762400-38763200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:38762400-38763600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:38762400-38763800	Active TSS	Brain Hippocampus Middle	brain
26	chr2:38762600-38763000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:38762600-38763000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:38762600-38763000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:38762600-38763000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:38762600-38763000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:38762600-38763000	Active TSS	Brain Cingulate Gyrus	brain
32	chr2:38762600-38763000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:38762600-38763000	Enhancers	Colonic Mucosa	Colon
34	chr2:38762600-38763000	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr2:38762600-38763200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:38762600-38763200	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr2:38762600-38763400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:38762800-38763000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:38762800-38763000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
40	chr2:38762800-38763000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr2:38762800-38763000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:38762800-38763000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr2:38762800-38763000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
44	chr2:38762800-38763000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:38762800-38763000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:38762800-38763000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:38762800-38763000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:38762800-38763000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:38762800-38763000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:38762800-38763000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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