Variant report

Variant	rs71558370
Chromosome Location	chr6:109776903-109776904
allele	G/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	PAX5	chr6:109776751-109776908	GM12878	blood:	n/a	n/a
2	MAZ	chr6:109776533-109777442	HepG2	liver:	n/a	n/a
3	MAX	chr6:109776615-109777343	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr6:109776760-109776910	GM12872	blood:	n/a	n/a
5	RCOR1	chr6:109776521-109777529	K562	blood:	n/a	n/a
6	SIN3AK20	chr6:109776689-109777318	K562	blood:	n/a	n/a
7	EGR1	chr6:109776607-109777733	HCT-116	colon:	n/a	chr6:109776988-109777002 chr6:109777401-109777414 chr6:109777398-109777412 chr6:109777401-109777414 chr6:109777402-109777411 chr6:109777401-109777411 chr6:109777401-109777414
8	POLR2A	chr6:109776685-109776930	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:109776707-109777269	PFSK-1	brain:	n/a	n/a
10	POU2F2	chr6:109776602-109776949	GM12878	blood:	n/a	chr6:109776731-109776743
11	POLR2A	chr6:109776353-109777494	H1-hESC	embryonic stem cell:	n/a	n/a
12	CCNT2	chr6:109776686-109777656	K562	blood:	n/a	n/a
13	HCFC1	chr6:109776653-109777622	K562	blood:	n/a	n/a
14	POLR2A	chr6:109776509-109777731	SK-N-MC	brain:	n/a	n/a
15	E2F6	chr6:109776618-109777468	K562	blood:	n/a	chr6:109776725-109776735
16	POLR2A	chr6:109776373-109778645	Hela-S3	cervix:	n/a	n/a
17	PML	chr6:109776605-109776941	GM12878	blood:	n/a	n/a
18	EBF1	chr6:109775690-109776939	GM12878	blood:	n/a	n/a
19	ZBTB7A	chr6:109776412-109777558	ECC-1	luminal epithelium:	n/a	chr6:109777453-109777462
20	POLR2A	chr6:109776602-109777449	K562	blood:	n/a	n/a
21	MAX	chr6:109776816-109777551	K562	blood:	n/a	n/a
22	POLR2A	chr6:109775787-109777267	IMR90	lung:	n/a	n/a
23	POLR2A	chr6:109775370-109776972	GM12892	blood:	n/a	n/a
24	HMGN3	chr6:109776667-109777467	K562	blood:	n/a	n/a
25	POLR2A	chr6:109774791-109778612	GM12892	blood:	n/a	n/a
26	PAX5	chr6:109776557-109776930	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:109776640-109777474	K562	blood:	n/a	n/a
28	SIN3AK20	chr6:109776245-109776954	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr6:109776700-109777224	Hela-S3	cervix:	n/a	n/a
30	GABPA	chr6:109776532-109777144	MCF-7	breast:	n/a	n/a
31	POLR2A	chr6:109776462-109777446	SK-N-SH	brain:	n/a	n/a
32	MYC	chr6:109776627-109777089	MCF-7	breast:	n/a	n/a
33	YY1	chr6:109776715-109777249	GM12878	blood:	n/a	chr6:109776728-109776739 chr6:109776883-109776892
34	POLR2A	chr6:109775261-109777757	GM19099	blood:	n/a	n/a
35	PAX5	chr6:109776632-109776966	GM12892	blood:	n/a	n/a
36	MTA3	chr6:109774944-109778262	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:109775300-109777378	NB4	blood:	n/a	n/a
38	REST	chr6:109775578-109777923	H1-neurons	neurons:	n/a	chr6:109776434-109776452 chr6:109777410-109777423 chr6:109775591-109775611 chr6:109777413-109777426 chr6:109775592-109775610
39	POLR2A	chr6:109775074-109777912	GM12878	blood:	n/a	n/a
40	RELA	chr6:109775723-109777443	GM10847	blood:	n/a	n/a
41	PAX5	chr6:109776583-109776957	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:109775718-109777473	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr6:109776235-109776947	GM12891	blood:	n/a	n/a
44	GABPA	chr6:109776625-109776972	H1-hESC	embryonic stem cell:	n/a	n/a
45	ATF2	chr6:109776302-109777053	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:109776624-109777476	K562	blood:	n/a	n/a
47	POLR2A	chr6:109774855-109777633	GM12892	blood:	n/a	n/a
48	ELK1	chr6:109776765-109776965	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr6:109776468-109777509	Gliobla	brain:	n/a	n/a
50	POU2F2	chr6:109776719-109776975	GM12878	blood:	n/a	chr6:109776731-109776743

No.	Distal block	Cell Line	Cell type
1	chr6:109703037..109705174-chr6:109776212..109778845,2	K562	blood:
2	chr6:109750346..109753133-chr6:109776216..109778124,3	K562	blood:
3	chr6:109703058..109705958-chr6:109774873..109777253,2	MCF-7	breast:
4	chr12:7052933..7053575-chr6:109776407..109777288,2	HCT-116	colon:
5	chr6:109775795..109777582-chr6:109802976..109804493,2	MCF-7	breast:
6	chr6:109753662..109755641-chr6:109776640..109778419,2	K562	blood:

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000185250	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000239160	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs34533653	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4428538	0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395145	chr6:109775784-109778832	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs71558370	ENSG00000135596	cis	multi-tissue	Pritchard
rs71558370	SMPD2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109775200-109778400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:109775400-109777400	Active TSS	HSMM	muscle
3	chr6:109775400-109777600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:109775400-109777800	Active TSS	NHDF-Ad	bronchial
5	chr6:109775600-109777600	Active TSS	Aorta	Aorta
6	chr6:109775600-109777800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
7	chr6:109775600-109778400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr6:109775800-109777600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr6:109775800-109777600	Active TSS	Fetal Kidney	kidney
10	chr6:109775800-109777600	Active TSS	Left Ventricle	heart
11	chr6:109775800-109777600	Active TSS	Hela-S3	cervix
12	chr6:109775800-109777800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:109775800-109777800	Active TSS	Brain Angular Gyrus	brain
14	chr6:109775800-109777800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:109775800-109778000	Active TSS	Small Intestine	intestine
16	chr6:109775800-109778800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:109775800-109778800	Active TSS	Psoas Muscle	Psoas
18	chr6:109776000-109777200	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr6:109776000-109777200	Active TSS	Primary B cells from cord blood	blood
20	chr6:109776000-109777200	Active TSS	Primary hematopoietic stem cells	blood
21	chr6:109776000-109777200	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr6:109776000-109777200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:109776000-109777200	Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr6:109776000-109777200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:109776000-109777200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:109776000-109777200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr6:109776000-109777200	Active TSS	Osteobl	bone
28	chr6:109776000-109777400	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr6:109776000-109777400	Active TSS	Primary B cells from peripheral blood	blood
30	chr6:109776000-109777400	Active TSS	Primary T cells from cord blood	blood
31	chr6:109776000-109777400	Active TSS	Brain Hippocampus Middle	brain
32	chr6:109776000-109777400	Active TSS	Fetal Brain Female	brain
33	chr6:109776000-109777400	Active TSS	Fetal Intestine Small	intestine
34	chr6:109776000-109777400	Active TSS	Lung	lung
35	chr6:109776000-109777600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:109776000-109777600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:109776000-109777600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:109776000-109777600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:109776000-109777600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:109776000-109777600	Active TSS	Brain Anterior Caudate	brain
41	chr6:109776000-109777600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:109776000-109777600	Active TSS	Brain Substantia Nigra	brain
43	chr6:109776000-109777600	Active TSS	Colon Smooth Muscle	Colon
44	chr6:109776000-109777600	Active TSS	Fetal Intestine Large	intestine
45	chr6:109776000-109777600	Active TSS	Fetal Lung	lung
46	chr6:109776000-109777600	Active TSS	Gastric	stomach
47	chr6:109776000-109777600	Active TSS	Ovary	ovary
48	chr6:109776000-109777600	Active TSS	Right Atrium	heart
49	chr6:109776000-109777600	Active TSS	GM12878-XiMat	blood
50	chr6:109776000-109777600	Active TSS	HepG2	liver

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