Variant report

Variant	rs73410003
Chromosome Location	chr6:33267014-33267015
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	EBF1	chr6:33266838-33267418	GM12878	blood:	n/a	chr6:33267109-33267122
2	RFX5	chr6:33266834-33267582	K562	blood:	n/a	n/a
3	POLR2A	chr6:33266502-33268161	GM12891	blood:	n/a	n/a
4	MEF2A	chr6:33266658-33267552	GM12878	blood:	n/a	n/a
5	CHD2	chr6:33266641-33267834	Hela-S3	cervix:	n/a	chr6:33266785-33266795
6	EBF1	chr6:33266826-33267616	GM12878	blood:	n/a	chr6:33267109-33267122
7	ELF1	chr6:33266923-33267638	A549	lung:	n/a	n/a
8	POLR2A	chr6:33266468-33268082	HepG2	liver:	n/a	n/a
9	BCLAF1	chr6:33266871-33267894	K562	blood:	n/a	n/a
10	MXI1	chr6:33266919-33267776	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:33265138-33268830	K562	blood:	n/a	n/a
12	NFIC	chr6:33266527-33267944	SK-N-SH	brain:	n/a	n/a
13	FOXM1	chr6:33266725-33267950	GM12878	blood:	n/a	n/a
14	RELA	chr6:33266794-33267886	GM19193	blood:	n/a	chr6:33267169-33267178 chr6:33267169-33267178
15	RXRA	chr6:33266967-33267266	GM12878	blood:	n/a	chr6:33267200-33267220
16	SIN3A	chr6:33266642-33268054	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF3	chr6:33266772-33267385	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:33266373-33268015	H1-neurons	neurons:	n/a	n/a
19	HDAC2	chr6:33266403-33267380	K562	blood:	n/a	n/a
20	GATA3	chr6:33266732-33267913	A549	lung:	n/a	chr6:33266832-33266842
21	SP1	chr6:33266835-33267487	H1-hESC	embryonic stem cell:	n/a	chr6:33267209-33267219 chr6:33267192-33267206 chr6:33267008-33267022 chr6:33267208-33267220 chr6:33267205-33267219 chr6:33267208-33267220 chr6:33267210-33267219 chr6:33267209-33267218 chr6:33267209-33267219 chr6:33267210-33267219 chr6:33267193-33267202
22	CHD2	chr6:33266473-33267793	GM12878	blood:	n/a	chr6:33266785-33266795
23	REST	chr6:33266952-33267742	PFSK-1	brain:	n/a	chr6:33267206-33267219
24	E2F6	chr6:33266564-33267909	K562	blood:	n/a	chr6:33266898-33266908 chr6:33266785-33266794 chr6:33267190-33267202 chr6:33267209-33267218 chr6:33267189-33267200
25	MAX	chr6:33266455-33268231	MCF-7	breast:	n/a	chr6:33267194-33267204
26	YY1	chr6:33267001-33268078	SK-N-SH_RA	brain:	n/a	chr6:33267209-33267218
27	E2F4	chr6:33266775-33267478	MCF10A-Er-Src	breast:	n/a	chr6:33266898-33266908 chr6:33266785-33266794 chr6:33267189-33267200 chr6:33267190-33267202 chr6:33267209-33267218
28	CEBPD	chr6:33266304-33268107	K562	blood:	n/a	n/a
29	PML	chr6:33266732-33268162	MCF-7	breast:	n/a	n/a
30	MAX	chr6:33266529-33267890	K562	blood:	n/a	chr6:33267194-33267204
31	YY1	chr6:33266701-33267795	SK-N-SH_RA	brain:	n/a	chr6:33267209-33267218
32	TAL1	chr6:33266589-33268031	K562	blood:	n/a	n/a
33	CHD2	chr6:33266987-33267701	H1-hESC	embryonic stem cell:	n/a	n/a
34	ETS1	chr6:33266756-33267489	GM12878	blood:	n/a	chr6:33267063-33267079 chr6:33267207-33267218 chr6:33267230-33267239 chr6:33267230-33267239 chr6:33267230-33267239 chr6:33267070-33267087 chr6:33267230-33267239 chr6:33267261-33267270
35	JUN	chr6:33264507-33268241	K562	blood:	n/a	chr6:33264795-33264808 chr6:33267162-33267176 chr6:33266833-33266842
36	POLR2A	chr6:33266414-33268204	GM12891	blood:	n/a	n/a
37	ZBTB33	chr6:33266886-33267829	SK-N-SH	brain:	n/a	n/a
38	HEY1	chr6:33266413-33268113	HepG2	liver:	n/a	n/a
39	TEAD4	chr6:33266970-33267324	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr6:33266389-33268848	HepG2	liver:	n/a	n/a
41	REST	chr6:33266921-33267483	PFSK-1	brain:	n/a	chr6:33267206-33267219
42	RELA	chr6:33266717-33267887	GM18951	blood:	n/a	chr6:33267169-33267178 chr6:33267169-33267178
43	SIX5	chr6:33266775-33267408	A549	lung:	n/a	n/a
44	POLR2A	chr6:33266795-33268068	PBDE	blood:	n/a	n/a
45	FOSL2	chr6:33266840-33267583	A549	lung:	n/a	chr6:33267162-33267176
46	SIN3AK20	chr6:33266989-33267416	K562	blood:	n/a	n/a
47	POLR2A	chr6:33266392-33268195	GM12891	blood:	n/a	n/a
48	TAF1	chr6:33266954-33267739	SK-N-SH	brain:	n/a	n/a
49	MAX	chr6:33266599-33267835	GM12878	blood:	n/a	chr6:33267194-33267204
50	EGR1	chr6:33266945-33267367	GM12878	blood:	n/a	chr6:33267194-33267207 chr6:33267209-33267219 chr6:33267194-33267207 chr6:33267191-33267205 chr6:33267193-33267208

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33266969-33267019	HAEpiC	amniotic membrane:	n/a
2	chr6:33266964-33267014	HIPEpiC	eye:	n/a
3	chr6:33266969-33267019	HCM	heart:	n/a
4	chr6:33266964-33267014	ProgFib	skin:	n/a
5	chr6:33266969-33267019	HCT-116	colon:	n/a
6	chr6:33266969-33267019	ECC-1	luminal epithelium:	n/a
7	chr6:33266964-33267014	GM12891	blood:	n/a
8	chr6:33266964-33267014	AG09309	skin:	n/a
9	chr6:33266969-33267019	SK-N-SH	brain:	n/a
10	chr6:33266964-33267014	BE2_C	brain:	n/a
11	chr6:33266964-33267014	ECC-1	luminal epithelium:	n/a
12	chr6:33266969-33267019	HEK293	kidney:	embryo
13	chr6:33266969-33267019	NH-A	brain:	n/a
14	chr6:33266969-33267019	K562	blood:	n/a
15	chr6:33266969-33267019	GM12878	blood:	n/a
16	chr6:33266964-33267014	PANC-1	pancreas:	n/a
17	chr6:33266969-33267019	PFSK-1	brain:	n/a
18	chr6:33266969-33267019	Caco-2	colon:	n/a
19	chr6:33266969-33267019	RPTEC	kidney:	n/a
20	chr6:33266969-33267019	AG04449	skin:	fetal
21	chr6:33266964-33267014	GM12892	blood:	n/a
22	chr6:33266964-33267014	HNPCEpiC	eye:	n/a
23	chr6:33266964-33267014	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:33266964-33267014	K562	blood:	n/a
25	chr6:33266964-33267014	SK-N-SH_RA	brain:	n/a
26	chr6:33266969-33267019	A549	lung:	n/a
27	chr6:33266969-33267019	SKMC	muscle:	n/a
28	chr6:33266964-33267014	Caco-2	colon:	n/a
29	chr6:33266964-33267014	HAEpiC	amniotic membrane:	n/a
30	chr6:33266964-33267014	HCM	heart:	n/a
31	chr6:33266964-33267014	AoSMC	blood vessel:	n/a
32	chr6:33266964-33267014	Hepatocyte	liver:	n/a
33	chr6:33266964-33267014	SKMC	muscle:	n/a
34	chr6:33266969-33267019	GM19239	blood:	n/a
35	chr6:33266964-33267014	U87	brain:	n/a
36	chr6:33266964-33267014	NB4	blood:	n/a
37	chr6:33266964-33267014	IMR90	lung:	fetal
38	chr6:33266969-33267019	AG10803	skin:	n/a
39	chr6:33266964-33267014	HCT-116	colon:	n/a
40	chr6:33266964-33267014	BJ	skin:	n/a
41	chr6:33266969-33267019	HEEpiC	esophagus:	n/a
42	chr6:33266964-33267014	HL-60	blood:	n/a
43	chr6:33266964-33267014	SK-N-SH	brain:	n/a
44	chr6:33266969-33267019	HPAEpiC	pulmonary alveolar:	n/a
45	chr6:33266969-33267019	PrEC	prostate:	n/a
46	chr6:33266969-33267019	AG09319	gingival:	n/a
47	chr6:33266969-33267019	MCF-7	breast:	n/a
48	chr6:33266964-33267014	T-47D	breast:	n/a
49	chr6:33266969-33267019	T-47D	breast:	n/a
50	chr6:33266964-33267014	AG04449	skin:	fetal

No.	Distal block	Cell Line	Cell type
1	chr6:33170673..33173201-chr6:33265164..33267803,3	MCF-7	breast:
2	chr6:33165372..33170767-chr6:33266115..33268730,6	K562	blood:
3	chr6:33266968..33267861-chr6:33285581..33286219,2	MCF-7	breast:
4	chr6:33264374..33267492-chr6:33422246..33424652,3	K562	blood:
5	chr6:33265888..33267696-chr9:132249173..132251354,2	MCF-7	breast:
6	chr6:32936010..32942689-chr6:33263698..33267271,9	MCF-7	breast:
7	chr6:33214841..33218494-chr6:33265669..33268981,6	K562	blood:
8	chr6:33263073..33268205-chr6:33376944..33380191,7	MCF-7	breast:
9	chr6:33176119..33178569-chr6:33265606..33267616,2	K562	blood:
10	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
11	chr6:33266975..33267589-chr8:124407959..124408629,2	Hela-S3	cervix:
12	chr6:33265365..33267205-chr6:33677898..33679962,2	K562	blood:
13	chr6:33265384..33269852-chr6:33356528..33361842,9	K562	blood:
14	chr6:32938856..32941327-chr6:33266126..33268647,2	MCF-7	breast:
15	chr3:49059217..49060086-chr6:33266878..33267523,2	Hela-S3	cervix:
16	chr6:33171180..33174226-chr6:33263989..33267648,4	K562	blood:
17	chr6:33264179..33271329-chr6:33356528..33360865,9	K562	blood:
18	chr6:33167814..33169961-chr6:33266237..33268419,3	MCF-7	breast:
19	chr6:33174866..33177619-chr6:33265606..33267266,2	K562	blood:
20	chr6:33264302..33268972-chr6:33371896..33376016,7	MCF-7	breast:
21	chr6:32941801..32944425-chr6:33264860..33267415,2	MCF-7	breast:
22	chr6:33264068..33267385-chr6:33357975..33361447,5	MCF-7	breast:
23	chr6:33257047..33258013-chr6:33266596..33267410,2	MCF-7	breast:
24	chr12:120729117..120730903-chr6:33265200..33267193,2	MCF-7	breast:
25	chr6:33167108..33170090-chr6:33265777..33268521,5	K562	blood:
26	chr6:33039965..33042578-chr6:33266503..33268028,2	MCF-7	breast:
27	chr6:32938391..32941384-chr6:33264154..33267922,4	K562	blood:
28	chr6:33264410..33268847-chr6:33383674..33387403,5	MCF-7	breast:
29	chr6:33239253..33239873-chr6:33266778..33267558,2	Hela-S3	cervix:
30	chr6:33215839..33219931-chr6:33265339..33267743,5	MCF-7	breast:
31	chr6:33263619..33269524-chr6:33392449..33400505,13	K562	blood:
32	chr6:33264378..33268881-chr6:33383627..33388443,14	K562	blood:

Variant related genes	Relation type
RGL2	TF binding region
RGL2	CpG island
ENSG00000263756	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000231389	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000204054	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000156802	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000204231	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs3173275	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56999860	0.82[AFR][1000 genomes]
rs57582515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57745261	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58283032	0.83[AFR][1000 genomes]
rs58759132	0.97[AFR][1000 genomes]
rs58883992	0.98[AFR][1000 genomes]
rs59097151	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59142568	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59368071	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59531270	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60170976	0.98[AFR][1000 genomes]
rs60813085	0.88[AFR][1000 genomes]
rs6906693	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6908509	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6920095	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6931141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408048	0.88[AFR][1000 genomes]
rs73408053	0.90[AFR][1000 genomes]
rs73408061	0.97[AFR][1000 genomes]
rs73408065	0.97[AFR][1000 genomes]
rs73408067	0.97[AFR][1000 genomes]
rs73410010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410043	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410049	0.91[AFR][1000 genomes];1.00[AMR][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	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33264600-33268200	Active TSS	Fetal Kidney	kidney
2	chr6:33264800-33268200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:33264800-33268400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:33264800-33268600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:33264800-33268600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:33264800-33269000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:33264800-33269000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:33265000-33267600	Active TSS	Brain Substantia Nigra	brain
9	chr6:33265000-33268000	Active TSS	Lung	lung
10	chr6:33265000-33268200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:33265000-33268200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:33265000-33268200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:33265000-33268200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:33265000-33268200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr6:33265000-33268200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:33265000-33268200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr6:33265000-33268200	Active TSS	Brain Cingulate Gyrus	brain
18	chr6:33265000-33268400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:33265000-33268600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:33265200-33267600	Active TSS	Fetal Intestine Small	intestine
21	chr6:33265200-33267800	Active TSS	Placenta Amnion	Placenta Amnion
22	chr6:33265200-33268000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:33265200-33268000	Active TSS	Brain Hippocampus Middle	brain
24	chr6:33265200-33268000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr6:33265200-33268200	Active TSS	Brain Angular Gyrus	brain
26	chr6:33265200-33268200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr6:33265200-33268200	Active TSS	Gastric	stomach
28	chr6:33265200-33268400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr6:33265200-33268400	Active TSS	Psoas Muscle	Psoas
30	chr6:33265400-33267600	Active TSS	Colon Smooth Muscle	Colon
31	chr6:33265400-33267600	Active TSS	Pancreas	Pancrea
32	chr6:33265400-33267800	Active TSS	Aorta	Aorta
33	chr6:33265400-33268000	Active TSS	Ovary	ovary
34	chr6:33265400-33268200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:33265400-33268200	Active TSS	Fetal Lung	lung
36	chr6:33265400-33268200	Active TSS	NHDF-Ad	bronchial
37	chr6:33265400-33268400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:33265400-33268400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:33265400-33268400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:33265400-33268400	Active TSS	Esophagus	oesophagus
41	chr6:33265400-33268400	Active TSS	Fetal Intestine Large	intestine
42	chr6:33265600-33267400	Active TSS	Colonic Mucosa	Colon
43	chr6:33265600-33267400	Active TSS	Duodenum Mucosa	Duodenum
44	chr6:33265600-33267400	Active TSS	GM12878-XiMat	blood
45	chr6:33265600-33267600	Active TSS	Primary monocytes fromperipheralblood	blood
46	chr6:33265600-33267600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:33265600-33267600	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr6:33265600-33267600	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr6:33265600-33267600	Active TSS	Spleen	Spleen
50	chr6:33265600-33267600	Active TSS	Monocytes-CD14+_RO01746	blood

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