Variant report

Variant	rs7893335
Chromosome Location	chr10:99259977-99259978
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	SIN3A	chr10:99257350-99259994	H1-hESC	embryonic stem cell:	n/a	chr10:99259344-99259357 chr10:99258820-99258831 chr10:99258406-99258417
2	POLR2A	chr10:99257185-99260373	HUVEC	blood vessel:	n/a	n/a
3	SPI1	chr10:99259477-99260074	HL-60	blood:	n/a	n/a
4	CEBPB	chr10:99259820-99260101	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:99259866-99260251	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr10:99259853-99260225	HUVEC	blood vessel:	n/a	n/a
7	CEBPB	chr10:99259681-99260096	HepG2	liver:	n/a	n/a
8	CEBPB	chr10:99259617-99260168	IMR90	lung:	n/a	n/a
9	CEBPB	chr10:99259925-99260097	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr10:99259888-99260064	HepG2	liver:	n/a	n/a
11	RCOR1	chr10:99259939-99260103	HepG2	liver:	n/a	n/a
12	MXI1	chr10:99257094-99260380	IMR90	lung:	n/a	n/a
13	MYC	chr10:99257355-99260136	NB4	blood:	n/a	chr10:99258254-99258265 chr10:99258920-99258930 chr10:99258255-99258264 chr10:99259189-99259199 chr10:99258671-99258681 chr10:99259326-99259336

No.	Distal block	Cell Line	Cell type
1	chr10:99159358..99162440-chr10:99256931..99260180,3	MCF-7	breast:
2	chr10:99205621..99207743-chr10:99257584..99260294,2	MCF-7	breast:
3	chr10:99258633..99260480-chr10:99272393..99275026,3	MCF-7	breast:
4	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
5	chr10:99158733..99161055-chr10:99257726..99260280,2	MCF-7	breast:
6	chr10:99254835..99256478-chr10:99258857..99262357,3	MCF-7	breast:
7	chr10:99259143..99261299-chr10:99264874..99266683,2	K562	blood:

Variant related genes	Relation type
MMS19	TF binding region
ENSG00000171307	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000165887	Chromatin interaction
ENSG00000231970	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10786351	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10882937	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs10882939	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs10882943	0.86[ASN][1000 genomes]
rs10882944	0.86[ASN][1000 genomes]
rs10882946	0.86[ASN][1000 genomes]
rs10882959	0.82[MEX][hapmap]
rs10882962	0.82[MEX][hapmap]
rs11189233	0.85[ASN][1000 genomes]
rs11189238	0.87[ASN][1000 genomes]
rs11189244	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189245	0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11189249	0.96[YRI][hapmap]
rs11189253	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11189259	0.82[MEX][hapmap]
rs11189275	0.88[MEX][hapmap]
rs12221474	0.82[MEX][hapmap]
rs12415482	0.80[ASN][1000 genomes]
rs1572860	0.88[MEX][hapmap]
rs17112814	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs17112841	0.82[AFR][1000 genomes]
rs2275583	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4917772	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4919104	0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs59109814	0.80[ASN][1000 genomes]
rs7084687	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7096611	1.00[CEU][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7902642	0.82[MEX][hapmap]
rs7915501	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3440915	chr10:99257587-99260135	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7893335	RRP12	cis	cerebellum	SCAN
rs7893335	CC2D2B	cis	parietal	SCAN
rs7893335	CCNJ	cis	cerebellum	SCAN
rs7893335	RRP12	cis	parietal	SCAN
rs7893335	MMS19	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99256800-99260000	Active TSS	Aorta	Aorta
2	chr10:99257000-99260400	Active TSS	Brain Angular Gyrus	brain
3	chr10:99257000-99260400	Active TSS	HSMM	muscle
4	chr10:99257200-99260000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:99257200-99260000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr10:99257400-99260000	Active TSS	Esophagus	oesophagus
7	chr10:99257400-99260000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:99257400-99260000	Active TSS	Ovary	ovary
9	chr10:99257600-99260000	Active TSS	Gastric	stomach
10	chr10:99258400-99260000	Active TSS	Right Atrium	heart
11	chr10:99258800-99260000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
12	chr10:99258800-99260200	Bivalent/Poised TSS	Thymus	Thymus
13	chr10:99258800-99260400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr10:99259000-99260000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:99259000-99260000	Bivalent Enhancer	Fetal Brain Male	brain
16	chr10:99259000-99260000	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr10:99259200-99260000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr10:99259200-99260000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:99259200-99260000	Flanking Active TSS	Hela-S3	cervix
20	chr10:99259400-99260000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr10:99259400-99260000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr10:99259400-99260000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr10:99259400-99260000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
24	chr10:99259400-99260000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
25	chr10:99259400-99260200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr10:99259400-99260200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr10:99259400-99260600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr10:99259600-99260000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr10:99259600-99260000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:99259600-99260000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr10:99259600-99260000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:99259600-99260000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
33	chr10:99259600-99260000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr10:99259600-99260000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
35	chr10:99259600-99260000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:99259600-99260000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
37	chr10:99259600-99260000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:99259600-99260000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr10:99259600-99260000	Flanking Active TSS	Liver	Liver
40	chr10:99259600-99260000	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr10:99259600-99260000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
42	chr10:99259600-99260000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
43	chr10:99259600-99260000	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr10:99259600-99260000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
45	chr10:99259600-99260200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr10:99259600-99260200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:99259600-99260200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr10:99259600-99260200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr10:99259600-99260200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr10:99259600-99260200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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