Variant report

Variant	rs12190029
Chromosome Location	chr6:33749152-33749153
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:33749132-33749481	Hela-S3	cervix:	n/a	n/a
2	FOXM1	chr6:33748875-33749913	ECC-1	luminal epithelium:	n/a	n/a
3	JUND	chr6:33748914-33749685	HCT-116	colon:	n/a	n/a
4	POLR2A	chr6:33748785-33749736	HUVEC	blood vessel:	n/a	n/a
5	GTF2F1	chr6:33749031-33749545	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr6:33749109-33749592	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOS	chr6:33749150-33749479	MCF10A-Er-Src	breast:	n/a	chr6:33749313-33749324
8	YY1	chr6:33749070-33749769	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP1	chr6:33749016-33749639	A549	lung:	n/a	n/a
10	JUND	chr6:33748955-33749660	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr6:33749073-33749706	H1-hESC	embryonic stem cell:	n/a	n/a
12	ESR1	chr6:33749076-33749596	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr6:33749128-33749491	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:33749047-33750161	HepG2	liver:	n/a	n/a
15	FOSL2	chr6:33749018-33749619	SK-N-SH	brain:	n/a	n/a
16	YY1	chr6:33749095-33749797	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr6:33749142-33749508	HCT-116	colon:	n/a	n/a
18	ESR1	chr6:33749057-33749735	ECC-1	luminal epithelium:	n/a	n/a
19	RAD21	chr6:33749109-33749594	H1-hESC	embryonic stem cell:	n/a	n/a
20	USF2	chr6:33749132-33749388	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:33748956-33749295	HepG2	liver:	n/a	n/a
22	EP300	chr6:33748809-33750016	ECC-1	luminal epithelium:	n/a	n/a
23	MEF2A	chr6:33748980-33749611	SK-N-SH	brain:	n/a	n/a
24	SIN3AK20	chr6:33749130-33749510	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr6:33748997-33749650	A549	lung:	n/a	n/a
26	NFIC	chr6:33748743-33749970	ECC-1	luminal epithelium:	n/a	n/a
27	TCF12	chr6:33748935-33750266	ECC-1	luminal epithelium:	n/a	chr6:33750172-33750180
28	JUND	chr6:33748937-33749638	HCT-116	colon:	n/a	n/a
29	TCF7L2	chr6:33748896-33749617	Hela-S3	cervix:	n/a	n/a
30	JUND	chr6:33748868-33749724	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr6:33748964-33749727	HUVEC	blood vessel:	n/a	n/a
32	RAD21	chr6:33749129-33749503	Hela-S3	cervix:	n/a	n/a
33	TFAP2C	chr6:33749074-33749747	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:33749055-33749491	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:33748974-33749518	SK-N-SH	brain:	n/a	n/a
36	TCF7L2	chr6:33748715-33749914	PANC-1	pancreas:	n/a	n/a
37	MAX	chr6:33749044-33749723	A549	lung:	n/a	n/a
38	RCOR1	chr6:33749145-33749551	Hela-S3	cervix:	n/a	n/a
39	MAX	chr6:33748874-33749995	ECC-1	luminal epithelium:	n/a	n/a
40	JUN	chr6:33749142-33749508	H1-hESC	embryonic stem cell:	n/a	n/a
41	FOXA2	chr6:33749061-33749428	A549	lung:	n/a	n/a
42	POLR2A	chr6:33748952-33750440	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr6:33749006-33750393	H1-hESC	embryonic stem cell:	n/a	n/a
44	JUND	chr6:33749082-33749483	H1-hESC	embryonic stem cell:	n/a	n/a
45	SMC3	chr6:33749008-33749587	Hela-S3	cervix:	n/a	n/a
46	ATF2	chr6:33749015-33749509	H1-hESC	embryonic stem cell:	n/a	n/a
47	TEAD4	chr6:33748730-33749936	ECC-1	luminal epithelium:	n/a	n/a
48	TEAD4	chr6:33749047-33749584	HCT-116	colon:	n/a	n/a
49	TEAD4	chr6:33749032-33749661	A549	lung:	n/a	n/a
50	POLR2A	chr6:33748936-33750243	HUVEC	blood vessel:	n/a	n/a

No data

Variant related genes	Relation type
LEMD2	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1359781	0.82[AFR][1000 genomes]
rs2296744	0.81[EUR][1000 genomes]
rs2296746	0.84[AFR][1000 genomes]
rs2296748	0.84[AFR][1000 genomes]
rs2395402	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4711349	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711355	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713679	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713682	0.81[AFR][1000 genomes]
rs6457741	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6922275	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6929696	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs747694	0.80[AMR][1000 genomes]
rs9357164	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9394166	0.84[AFR][1000 genomes]
rs9394167	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs943471	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs943474	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs943475	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs943478	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs943479	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 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	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
2	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
8	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:33740000-33752800	Strong transcription	Dnd41	blood
14	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:33740000-33753000	Strong transcription	HepG2	liver
16	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:33740200-33749200	Strong transcription	Gastric	stomach
20	chr6:33740200-33749400	Strong transcription	Lung	lung
21	chr6:33740200-33750000	Strong transcription	Pancreas	Pancrea
22	chr6:33740200-33751600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:33740200-33751800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:33740200-33752400	Strong transcription	Rectal Smooth Muscle	rectum
25	chr6:33740200-33752600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:33740200-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:33740200-33753400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
29	chr6:33740400-33749200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:33740400-33752600	Strong transcription	Colon Smooth Muscle	Colon
31	chr6:33740400-33752800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:33740400-33753200	Strong transcription	Aorta	Aorta
33	chr6:33740400-33753600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:33740600-33749200	Strong transcription	Adipose Nuclei	Adipose
35	chr6:33740600-33753000	Strong transcription	Liver	Liver
36	chr6:33740600-33753000	Strong transcription	Colonic Mucosa	Colon
37	chr6:33740600-33754200	Strong transcription	Fetal Intestine Large	intestine
38	chr6:33740600-33754200	Strong transcription	Fetal Intestine Small	intestine
39	chr6:33740800-33749200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:33741000-33751600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:33741000-33752600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:33741000-33753000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr6:33741000-33753200	Strong transcription	Fetal Brain Female	brain
44	chr6:33741000-33754000	Strong transcription	Fetal Thymus	thymus
45	chr6:33741400-33749400	Strong transcription	Placenta	Placenta
46	chr6:33741400-33753000	Strong transcription	Fetal Lung	lung
47	chr6:33741400-33753000	Strong transcription	Ovary	ovary
48	chr6:33741400-33753200	Strong transcription	Fetal Stomach	stomach
49	chr6:33741600-33749200	Strong transcription	Esophagus	oesophagus
50	chr6:33741600-33749400	Strong transcription	Fetal Muscle Leg	muscle

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