Variant report

Variant	rs10259650
Chromosome Location	chr7:38217295-38217296
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	MAZ	chr7:38217048-38219706	IMR90	lung:	n/a	chr7:38218254-38218263
2	NFIC	chr7:38217082-38218203	GM12878	blood:	n/a	n/a
3	REST	chr7:38217106-38218923	H1-neurons	neurons:	n/a	n/a
4	TBP	chr7:38217294-38218192	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:38217251-38218311	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:38217290-38218431	K562	blood:	n/a	n/a
7	RUNX3	chr7:38217266-38218690	GM12878	blood:	n/a	n/a
8	NFYA	chr7:38217255-38217991	K562	blood:	n/a	n/a
9	TCF7L2	chr7:38217276-38218192	PANC-1	pancreas:	n/a	n/a
10	TBL1XR1	chr7:38217263-38218148	K562	blood:	n/a	n/a
11	SP1	chr7:38217268-38218220	A549	lung:	n/a	chr7:38218172-38218186 chr7:38218175-38218187
12	MTA3	chr7:38217085-38218860	GM12878	blood:	n/a	n/a
13	MAX	chr7:38217167-38218458	A549	lung:	n/a	chr7:38218254-38218263
14	POLR2A	chr7:38217136-38218428	K562	blood:	n/a	n/a
15	SPI1	chr7:38217207-38218160	HL-60	blood:	n/a	chr7:38217574-38217581 chr7:38217694-38217707 chr7:38217573-38217582
16	POLR2A	chr7:38217219-38218300	SK-N-MC	brain:	n/a	n/a
17	RCOR1	chr7:38217116-38220211	IMR90	lung:	n/a	n/a
18	POLR2A	chr7:38217215-38218573	HUVEC	blood vessel:	n/a	n/a
19	SP1	chr7:38217258-38218434	HCT-116	colon:	n/a	chr7:38218172-38218186 chr7:38218175-38218187
20	MAX	chr7:38217264-38218256	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOSL2	chr7:38217275-38218279	A549	lung:	n/a	chr7:38217845-38217854
22	RCOR1	chr7:38217256-38218642	GM12878	blood:	n/a	n/a
23	SPI1	chr7:38217253-38217754	GM12878	blood:	n/a	chr7:38217574-38217581 chr7:38217694-38217707 chr7:38217573-38217582
24	CREB1	chr7:38217265-38218713	GM12878	blood:	n/a	chr7:38217843-38217856
25	POLR2A	chr7:38217272-38218488	GM19193	blood:	n/a	n/a
26	PML	chr7:38217212-38218675	GM12878	blood:	n/a	n/a
27	MXI1	chr7:38216789-38219828	IMR90	lung:	n/a	n/a
28	SPI1	chr7:38217232-38217742	GM12891	blood:	n/a	chr7:38217574-38217581 chr7:38217694-38217707 chr7:38217573-38217582
29	NFIC	chr7:38217235-38217787	GM12878	blood:	n/a	n/a
30	MAX	chr7:38217248-38218440	SK-N-SH	brain:	n/a	chr7:38218254-38218263
31	MAX	chr7:38217241-38218402	HepG2	liver:	n/a	chr7:38218254-38218263
32	IRF4	chr7:38217262-38217927	GM12878	blood:	n/a	n/a
33	MAX	chr7:38217277-38218736	GM12878	blood:	n/a	chr7:38218254-38218263
34	MAX	chr7:38217268-38218333	ECC-1	luminal epithelium:	n/a	chr7:38218254-38218263
35	POLR2A	chr7:38217174-38218406	U87	brain:	n/a	n/a
36	POLR2A	chr7:38217251-38218378	HL-60	blood:	n/a	n/a
37	E2F4	chr7:38217130-38218136	MCF10A-Er-Src	breast:	n/a	chr7:38217846-38217855 chr7:38217613-38217620 chr7:38217613-38217620 chr7:38217844-38217853 chr7:38217613-38217620
38	POLR2A	chr7:38217149-38218679	GM18505	blood:	n/a	n/a
39	NFYA	chr7:38217088-38218259	Hela-S3	cervix:	n/a	n/a
40	MAX	chr7:38217234-38218469	SK-N-SH	brain:	n/a	chr7:38218254-38218263
41	POLR2A	chr7:38217251-38218368	GM12892	blood:	n/a	n/a
42	MAX	chr7:38217223-38218307	A549	lung:	n/a	chr7:38218254-38218263
43	MXI1	chr7:38217278-38218701	GM12878	blood:	n/a	n/a
44	TAF1	chr7:38217229-38218416	ECC-1	luminal epithelium:	n/a	n/a
45	PBX3	chr7:38217225-38218293	SK-N-SH	brain:	n/a	chr7:38217733-38217753
46	REST	chr7:38217249-38218195	A549	lung:	n/a	n/a
47	EP300	chr7:38217254-38217891	A549	lung:	n/a	chr7:38217869-38217885
48	POLR2A	chr7:38217272-38218602	K562	blood:	n/a	n/a
49	MXI1	chr7:38216167-38220054	SK-N-SH	brain:	n/a	n/a
50	E2F6	chr7:38217091-38218241	A549	lung:	n/a	chr7:38217846-38217855 chr7:38217613-38217620 chr7:38217613-38217620 chr7:38217844-38217853 chr7:38217701-38217712 chr7:38217657-38217668 chr7:38217613-38217620

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:52450154..52450678-chr7:38217214..38217841,2	Hela-S3	cervix:
2	chr7:38216168..38217800-chr7:38379811..38381919,2	K562	blood:

Variant related genes	Relation type
STARD3NL	TF binding region
ENSG00000123358	Chromatin interaction
ENSG00000226212	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10230858	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260904	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10265214	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10269098	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10272537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769941	0.82[GIH][hapmap]
rs1990362	0.82[GIH][hapmap]
rs4624935	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973458	0.82[GIH][hapmap]
rs7787991	0.82[GIH][hapmap]
rs7794324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2762664	chr7:38201814-38228480	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10259650	STARD3NL	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38216800-38217800	Flanking Active TSS	Dnd41	blood
2	chr7:38216800-38218600	Active TSS	Fetal Kidney	kidney
3	chr7:38216800-38218800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:38217000-38217600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr7:38217000-38217600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr7:38217000-38217600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:38217000-38218600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr7:38217000-38218600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr7:38217000-38218600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr7:38217000-38218600	Active TSS	Fetal Brain Male	brain
11	chr7:38217000-38218800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:38217000-38218800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:38217000-38218800	Active TSS	Brain Angular Gyrus	brain
14	chr7:38217000-38218800	Active TSS	Fetal Brain Female	brain
15	chr7:38217000-38219200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:38217000-38219400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:38217000-38219400	Active TSS	GM12878-XiMat	blood
18	chr7:38217000-38219600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr7:38217000-38219800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr7:38217200-38217400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:38217200-38217400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr7:38217200-38217400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:38217200-38217400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr7:38217200-38217400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:38217200-38217400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr7:38217200-38217400	Flanking Active TSS	Fetal Heart	heart
27	chr7:38217200-38217400	Flanking Active TSS	Fetal Intestine Large	intestine
28	chr7:38217200-38217400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
29	chr7:38217200-38217400	Enhancers	Stomach Mucosa	stomach
30	chr7:38217200-38217400	Flanking Active TSS	HMEC	breast
31	chr7:38217200-38217400	Flanking Active TSS	NHDF-Ad	bronchial
32	chr7:38217200-38217400	Flanking Active TSS	NHLF	lung
33	chr7:38217200-38217600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:38217200-38217600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:38217200-38217600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr7:38217200-38217600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr7:38217200-38217600	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr7:38217200-38217600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr7:38217200-38217600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr7:38217200-38217600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr7:38217200-38217600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr7:38217200-38217600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:38217200-38217600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:38217200-38217600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr7:38217200-38217600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:38217200-38217600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr7:38217200-38217600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr7:38217200-38217600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr7:38217200-38217600	Flanking Active TSS	HSMM	muscle
50	chr7:38217200-38217600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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