Variant report

Variant	rs10993464
Chromosome Location	chr9:97808086-97808087
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	MAX	chr9:97806601-97808755	A549	lung:	n/a	n/a
2	EP300	chr9:97806767-97808285	A549	lung:	n/a	n/a
3	RAD21	chr9:97807955-97808442	H1-hESC	embryonic stem cell:	n/a	chr9:97808281-97808300 chr9:97808151-97808164
4	MYC	chr9:97808067-97808121	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr9:97808080-97808230	HEEpiC	esophagus:	n/a	n/a
6	POLR2A	chr9:97808069-97808123	MCF-7	breast:	n/a	n/a
7	TEAD4	chr9:97808030-97808413	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr9:97807940-97808321	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr9:97807983-97808227	ProgFib	skin:	n/a	n/a
10	SIN3A	chr9:97807278-97808405	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr9:97806630-97809069	A549	lung:	n/a	chr9:97807931-97807941 chr9:97807799-97807806 chr9:97807952-97807959 chr9:97806906-97806914
12	ATF3	chr9:97806811-97808484	A549	lung:	n/a	n/a
13	CTCF	chr9:97808080-97808230	HRE	kidney:	n/a	n/a
14	TCF7L2	chr9:97808026-97808500	PANC-1	pancreas:	n/a	n/a
15	YY1	chr9:97807779-97808429	A549	lung:	n/a	n/a
16	POLR2A	chr9:97807863-97808140	SK-N-SH	brain:	n/a	n/a
17	BCL3	chr9:97805869-97809192	A549	lung:	n/a	chr9:97807640-97807649
18	MAX	chr9:97808064-97808424	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr9:97808057-97808331	A549	lung:	n/a	n/a
20	POLR2A	chr9:97806627-97808676	A549	lung:	n/a	n/a
21	CTCF	chr9:97808080-97808370	BE2_C	brain:	n/a	chr9:97808280-97808298
22	CTCF	chr9:97806804-97809298	A549	lung:	n/a	chr9:97808280-97808298 chr9:97807606-97807619 chr9:97807066-97807075 chr9:97807801-97807814 chr9:97807525-97807538
23	POLR2A	chr9:97807991-97808351	A549	lung:	n/a	n/a
24	POLR2A	chr9:97808072-97808334	A549	lung:	n/a	n/a
25	SP1	chr9:97807128-97808432	A549	lung:	n/a	n/a
26	BCL3	chr9:97806825-97808589	A549	lung:	n/a	chr9:97807640-97807649
27	CTCF	chr9:97807980-97808130	SAEC	small airway:	n/a	n/a
28	POLR2A	chr9:97808081-97808341	A549	lung:	n/a	n/a
29	GATA3	chr9:97806950-97808848	A549	lung:	n/a	chr9:97808744-97808760 chr9:97807485-97807495 chr9:97808749-97808756 chr9:97808749-97808756 chr9:97808749-97808756 chr9:97808471-97808481 chr9:97808470-97808482 chr9:97808742-97808763
30	REST	chr9:97808025-97808655	A549	lung:	n/a	chr9:97808035-97808053
31	MAX	chr9:97807811-97808657	A549	lung:	n/a	n/a
32	SIN3AK20	chr9:97807893-97808349	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97772268..97775206-chr9:97807423..97809466,2	K562	blood:
2	chr9:97807151..97809032-chr9:97838332..97840072,2	MCF-7	breast:
3	chr9:97800986..97803575-chr9:97807961..97810868,3	K562	blood:
4	chr9:97803206..97809214-chr9:97809347..97813672,8	MCF-7	breast:
5	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
6	chr9:97802158..97803981-chr9:97806425..97808316,2	K562	blood:
7	chr9:97806251..97809142-chr9:97810861..97813740,3	MCF-7	breast:
8	chr9:97800135..97801967-chr9:97807867..97810456,2	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1004373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117370	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121760	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761366	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761368	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761369	0.82[EUR][1000 genomes]
rs10761372	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10993427	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412488	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564234	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571894	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571895	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061800	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404305	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404456	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3802456	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858089	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4537362	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743981	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743982	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744422	0.80[AMR][1000 genomes]
rs4744423	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744424	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744425	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744428	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744431	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744436	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479588	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479591	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479592	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020709	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7022452	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043705	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851173	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7854831	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863291	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865144	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7871218	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873479	0.80[AMR][1000 genomes]
rs7873567	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs962229	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10993464	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
3	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:97800000-97808600	Genic enhancers	Liver	Liver
8	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:97803000-97810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:97804000-97808800	Weak transcription	Fetal Kidney	kidney
11	chr9:97804000-97810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:97804400-97810400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:97804400-97810800	Weak transcription	K562	blood
14	chr9:97804800-97808200	Strong transcription	NH-A	brain
15	chr9:97804800-97808200	Strong transcription	NHLF	lung
16	chr9:97805000-97810000	Weak transcription	Brain Anterior Caudate	brain
17	chr9:97805200-97808400	Genic enhancers	Fetal Intestine Small	intestine
18	chr9:97805200-97810400	Weak transcription	Brain Angular Gyrus	brain
19	chr9:97805400-97810600	Weak transcription	Small Intestine	intestine
20	chr9:97805600-97810800	Weak transcription	GM12878-XiMat	blood
21	chr9:97806000-97808200	Genic enhancers	Fetal Stomach	stomach
22	chr9:97806000-97808400	Genic enhancers	Fetal Intestine Large	intestine
23	chr9:97806200-97808200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:97806200-97808200	Transcr. at gene 5' and 3'	A549	lung
25	chr9:97806400-97810600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:97806600-97808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:97806600-97808200	Enhancers	Psoas Muscle	Psoas
28	chr9:97806600-97810400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:97806800-97808200	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr9:97806800-97808200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:97806800-97808400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:97806800-97808400	Enhancers	Gastric	stomach
33	chr9:97807000-97808200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:97807000-97808200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr9:97807000-97808200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr9:97807000-97808200	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr9:97807000-97808400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:97807000-97810400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:97807000-97811000	Weak transcription	Stomach Mucosa	stomach
40	chr9:97807200-97808200	Enhancers	Right Ventricle	heart
41	chr9:97807200-97808400	Active TSS	Aorta	Aorta
42	chr9:97807200-97808400	Genic enhancers	Left Ventricle	heart
43	chr9:97807200-97808400	Flanking Active TSS	Pancreas	Pancrea
44	chr9:97807200-97809200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:97807200-97809800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:97807200-97809800	Weak transcription	HepG2	liver
47	chr9:97807200-97810000	Weak transcription	HMEC	breast
48	chr9:97807200-97810000	Weak transcription	HSMMtube	muscle
49	chr9:97807200-97810200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr9:97807200-97810200	Weak transcription	Hela-S3	cervix

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