Variant report

Variant	rs10168794
Chromosome Location	chr2:234293747-234293748
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	CTCF	chr2:234293656-234293766	GM19239	blood:	n/a	n/a
2	CTCF	chr2:234293700-234293850	GM12878	blood:	n/a	chr2:234293784-234293794
3	FOXA1	chr2:234293377-234293820	HepG2	liver:	n/a	n/a
4	CTCF	chr2:234293629-234293877	IMR90	lung:	n/a	chr2:234293784-234293794
5	POLR2A	chr2:234293034-234295804	GM18505	blood:	n/a	n/a
6	RAD21	chr2:234293628-234293795	SK-N-SH_RA	brain:	n/a	chr2:234293783-234293793
7	POLR2A	chr2:234293747-234294391	GM12891	blood:	n/a	n/a
8	CTCF	chr2:234293600-234293750	SK-N-SH_RA	brain:	n/a	chr2:234293626-234293639
9	STAT5A	chr2:234293658-234294893	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:234293276-234294756	GM15510	blood:	n/a	n/a
11	MAX	chr2:234293703-234293879	GM12878	blood:	n/a	n/a
12	FOXA1	chr2:234293476-234293836	HepG2	liver:	n/a	n/a
13	FOXA1	chr2:234293321-234293845	HepG2	liver:	n/a	n/a
14	CTCF	chr2:234293649-234293756	GM12891	blood:	n/a	n/a
15	ELF1	chr2:234293417-234294382	GM12878	blood:	n/a	n/a
16	CTCF	chr2:234293620-234293770	HCPEpiC	choroid plexus:	n/a	chr2:234293626-234293639
17	RAD21	chr2:234293609-234293870	SK-N-SH_RA	brain:	n/a	chr2:234293783-234293793
18	RAD21	chr2:234293627-234293821	IMR90	lung:	n/a	chr2:234293783-234293793
19	RUNX3	chr2:234293504-234295254	GM12878	blood:	n/a	n/a
20	MYC	chr2:234293431-234293825	MCF10A-Er-Src	breast:	n/a	chr2:234293701-234293710
21	POLR2A	chr2:234293493-234294860	GM12892	blood:	n/a	n/a
22	RAD21	chr2:234293617-234293771	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr2:234293640-234293790	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr2:234293700-234293850	HPAF	blood vessel:	n/a	chr2:234293784-234293794
25	FOXA1	chr2:234293384-234293785	HepG2	liver:	n/a	n/a
26	MAX	chr2:234293480-234294021	HepG2	liver:	n/a	chr2:234293879-234293888 chr2:234293880-234293887 chr2:234293701-234293710
27	POLR2A	chr2:234293409-234294421	GM12892	blood:	n/a	n/a
28	FOXA2	chr2:234293493-234293888	A549	lung:	n/a	n/a
29	CTCF	chr2:234293666-234293811	GM12878	blood:	n/a	chr2:234293784-234293794
30	RAD21	chr2:234293698-234293750	HepG2	liver:	n/a	n/a
31	MAX	chr2:234293731-234293805	NB4	blood:	n/a	n/a
32	MTA3	chr2:234293391-234295254	GM12878	blood:	n/a	n/a
33	CTCF	chr2:234293665-234293755	GM19238	blood:	n/a	n/a
34	CTCF	chr2:234293614-234293776	GM12892	blood:	n/a	chr2:234293626-234293639
35	MAX	chr2:234293362-234294525	A549	lung:	n/a	chr2:234294330-234294337 chr2:234293879-234293888 chr2:234293880-234293887 chr2:234293701-234293710 chr2:234294329-234294338
36	CTCF	chr2:234293687-234293760	GM19240	blood:	n/a	n/a
37	POLR2A	chr2:234293343-234297175	GM12891	blood:	n/a	n/a
38	CTCF	chr2:234293600-234293778	HepG2	liver:	n/a	chr2:234293626-234293639
39	POLR2A	chr2:234293457-234293756	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
2	chr2:234292070..234294223-chr2:234599510..234601905,2	MCF-7	breast:
3	chr2:234289741..234291350-chr2:234292115..234294515,2	K562	blood:

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10177112	1.00[JPT][hapmap]
rs10185174	1.00[ASN][1000 genomes]
rs10193542	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1037451	1.00[JPT][hapmap]
rs10929208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11892545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12467878	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13384932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391864	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs13400563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs13403169	0.88[CEU][hapmap]
rs13414407	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs13420976	1.00[ASN][1000 genomes]
rs13425849	0.88[CEU][hapmap]
rs13427703	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1542325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1901812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2124045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2289473	1.00[CHB][hapmap]
rs28437319	1.00[ASN][1000 genomes]
rs28605452	0.84[ASN][1000 genomes]
rs28657808	1.00[ASN][1000 genomes]
rs2924809	1.00[JPT][hapmap]
rs2971865	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3762586	0.84[ASN][1000 genomes]
rs3792095	0.84[ASN][1000 genomes]
rs3792104	1.00[CHB][hapmap]
rs3792105	1.00[CHB][hapmap]
rs4047198	1.00[JPT][hapmap]
rs4047199	1.00[JPT][hapmap]
rs4663698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56871749	1.00[ASN][1000 genomes]
rs57712949	1.00[ASN][1000 genomes]
rs58222850	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716988	1.00[JPT][hapmap]
rs6720619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6726184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6745134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73106630	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7422734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7572257	0.88[CEU][hapmap]
rs7588509	1.00[CHB][hapmap]
rs838557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs838558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs838561	1.00[JPT][hapmap]
rs838562	1.00[JPT][hapmap]

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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:234265000-234295000	Weak transcription	Osteobl	bone
3	chr2:234265200-234295000	Weak transcription	NH-A	brain
4	chr2:234266400-234294000	Weak transcription	Fetal Brain Male	brain
5	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:234278600-234293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:234278600-234294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:234278600-234294000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:234279200-234294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:234282400-234294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:234282400-234298000	Weak transcription	Dnd41	blood
17	chr2:234284000-234293800	Weak transcription	Colonic Mucosa	Colon
18	chr2:234284800-234295400	Weak transcription	Fetal Intestine Large	intestine
19	chr2:234285000-234295400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:234287400-234294800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:234289000-234307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:234289600-234294600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:234290200-234294800	Weak transcription	Small Intestine	intestine
24	chr2:234290600-234297000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr2:234290800-234294000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:234290800-234296800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr2:234291000-234297000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:234291200-234295800	Enhancers	Thymus	Thymus
29	chr2:234292000-234297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:234292200-234294000	Enhancers	Primary T cells from cord blood	blood
31	chr2:234292200-234294400	Genic enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:234292200-234294400	Enhancers	Ovary	ovary
33	chr2:234292200-234296400	Enhancers	Primary hematopoietic stem cells	blood
34	chr2:234292200-234296600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:234292200-234297200	Enhancers	Fetal Heart	heart
36	chr2:234292200-234297200	Enhancers	Left Ventricle	heart
37	chr2:234292400-234293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:234292400-234294600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:234292400-234294800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:234292400-234295800	Enhancers	K562	blood
41	chr2:234292400-234296000	Enhancers	Fetal Lung	lung
42	chr2:234292400-234296200	Enhancers	HepG2	liver
43	chr2:234292400-234296800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:234292400-234297200	Enhancers	Right Ventricle	heart
45	chr2:234292600-234294000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:234292600-234294000	Enhancers	Fetal Muscle Trunk	muscle
47	chr2:234292600-234294000	Enhancers	NHEK	skin
48	chr2:234292600-234294200	Genic enhancers	Monocytes-CD14+_RO01746	blood
49	chr2:234292600-234297000	Enhancers	Fetal Stomach	stomach
50	chr2:234292600-234297000	Enhancers	Fetal Thymus	thymus

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