Variant report

Variant	rs13197176
Chromosome Location	chr6:28129232-28129233
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	MTA3	chr6:28129150-28129862	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:28129207-28130008	GM19099	blood:	n/a	n/a
3	POLR2A	chr6:28129199-28129821	HEK293	kidney:	n/a	n/a
4	GABPA	chr6:28129081-28130063	HL-60	blood:	n/a	n/a
5	POLR2A	chr6:28129155-28129842	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:28129068-28130016	HL-60	blood:	n/a	n/a
7	POLR2A	chr6:28129160-28129900	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr6:28126889-28129797	HepG2	liver:	n/a	n/a
9	TEAD4	chr6:28129219-28129820	K562	blood:	n/a	chr6:28129677-28129686
10	POLR2A	chr6:28129112-28129876	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:28129217-28129795	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr6:28129177-28129995	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:28129214-28129803	GM18951	blood:	n/a	n/a
14	STAT5A	chr6:28129185-28129720	GM12878	blood:	n/a	chr6:28129503-28129523 chr6:28129374-28129381
15	CEBPD	chr6:28129205-28129741	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:28129175-28129881	SK-N-SH	brain:	n/a	n/a
17	HEY1	chr6:28129221-28129839	K562	blood:	n/a	n/a
18	HEY1	chr6:28129184-28129848	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:28128691-28129840	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:28129206-28129837	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:28129173-28129830	GM12891	blood:	n/a	n/a
22	MAX	chr6:28129210-28129831	NB4	blood:	n/a	n/a
23	POLR2A	chr6:28128782-28129787	U87	brain:	n/a	n/a
24	RAD21	chr6:28129220-28129862	H1-hESC	embryonic stem cell:	n/a	chr6:28129694-28129706
25	E2F6	chr6:28129151-28129807	H1-hESC	embryonic stem cell:	n/a	chr6:28129490-28129500
26	POLR2A	chr6:28129120-28129945	GM12878	blood:	n/a	n/a
27	SIN3AK20	chr6:28129139-28129790	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr6:28129215-28129837	GM19193	blood:	n/a	n/a
29	GABPA	chr6:28129217-28129772	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:28129189-28129826	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr6:28128776-28129787	U87	brain:	n/a	n/a
32	POLR2A	chr6:28129228-28129818	K562	blood:	n/a	n/a
33	WRNIP1	chr6:28129197-28129390	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:28129151-28129846	K562	blood:	n/a	n/a
35	PML	chr6:28129116-28129931	GM12878	blood:	n/a	n/a
36	SRF	chr6:28129224-28129787	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr6:28128832-28129989	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr6:28129171-28129919	K562	blood:	n/a	n/a
39	POLR2A	chr6:28129226-28129815	K562	blood:	n/a	n/a
40	POU2F2	chr6:28129219-28129827	GM12891	blood:	n/a	n/a
41	POLR2A	chr6:28129096-28129769	SK-N-SH	brain:	n/a	n/a
42	GABPA	chr6:28129152-28129924	K562	blood:	n/a	n/a
43	ELF1	chr6:28129231-28129736	GM12878	blood:	n/a	chr6:28129518-28129531 chr6:28129521-28129530 chr6:28129520-28129531
44	POLR2A	chr6:28128580-28129922	A549	lung:	n/a	n/a
45	MAX	chr6:28129170-28129918	K562	blood:	n/a	n/a
46	GABPA	chr6:28129222-28129826	K562	blood:	n/a	n/a
47	POLR2A	chr6:28129194-28129893	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:28129156-28129837	ECC-1	luminal epithelium:	n/a	n/a
49	MAX	chr6:28129223-28129798	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr6:28129219-28129888	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28109577..28112061-chr6:28128257..28130394,3	MCF-7	breast:
2	chr6:28126892..28131515-chr6:28301205..28304944,6	K562	blood:
3	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:

Variant related genes	Relation type
ZNF192P1	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs13195291	1.00[AMR][1000 genomes]
rs13197574	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13197633	1.00[AMR][1000 genomes]
rs13201308	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13203816	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13205911	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13217984	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34166054	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34371502	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34505829	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34588114	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34765154	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34832585	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35098436	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35345226	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35749575	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35781323	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35902873	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66886492	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67297533	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68188794	1.00[AMR][1000 genomes]
rs71559070	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71559072	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72846780	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72846794	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13197176	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13197176	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13197176	AL022393.7	cis	Muscle Skeletal	GTEx
rs13197176	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28122800-28129400	Weak transcription	Spleen	Spleen
2	chr6:28123800-28129600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:28127000-28134200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:28128800-28129400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:28128800-28129400	Flanking Active TSS	Dnd41	blood
6	chr6:28128800-28129600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:28128800-28129800	Active TSS	Brain Germinal Matrix	brain
8	chr6:28128800-28130000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:28129000-28129400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:28129000-28129400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:28129000-28129400	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr6:28129000-28129400	Active TSS	Thymus	Thymus
13	chr6:28129000-28129400	Flanking Active TSS	NHDF-Ad	bronchial
14	chr6:28129000-28129600	Active TSS	Duodenum Mucosa	Duodenum
15	chr6:28129000-28129600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr6:28129000-28129800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:28129000-28129800	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:28129000-28129800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:28129000-28129800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:28129000-28129800	Active TSS	NHEK	skin
21	chr6:28129000-28130000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:28129000-28130000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr6:28129000-28130000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:28129000-28130000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr6:28129000-28130000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr6:28129000-28130000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:28129000-28130000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28129000-28130000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:28129000-28130000	Active TSS	Fetal Intestine Large	intestine
30	chr6:28129000-28130000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr6:28129000-28130000	Active TSS	A549	lung
32	chr6:28129000-28130000	Active TSS	HepG2	liver
33	chr6:28129000-28130000	Active TSS	HMEC	breast
34	chr6:28129000-28130200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr6:28129000-28130200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:28129000-28130200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:28129000-28130200	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:28129000-28130200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:28129000-28130200	Active TSS	Fetal Brain Female	brain
40	chr6:28129000-28130200	Active TSS	Fetal Kidney	kidney
41	chr6:28129000-28130200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr6:28129000-28130400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:28129000-28130400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr6:28129000-28130400	Active TSS	Psoas Muscle	Psoas
45	chr6:28129000-28130400	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:28129000-28130600	Active TSS	GM12878-XiMat	blood
47	chr6:28129200-28129400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr6:28129200-28129400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr6:28129200-28129400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:28129200-28129400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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