Variant report

Variant	rs7871218
Chromosome Location	chr9:97807791-97807792
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	MAX	chr9:97806601-97808755	A549	lung:	n/a	n/a
2	EP300	chr9:97806767-97808285	A549	lung:	n/a	n/a
3	FOSL2	chr9:97806948-97807860	A549	lung:	n/a	n/a
4	POLR2A	chr9:97806933-97807902	A549	lung:	n/a	n/a
5	JUND	chr9:97806830-97807858	A549	lung:	n/a	n/a
6	SIN3A	chr9:97807278-97808405	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr9:97806630-97809069	A549	lung:	n/a	chr9:97807931-97807941 chr9:97807799-97807806 chr9:97807952-97807959 chr9:97806906-97806914
8	ATF3	chr9:97806811-97808484	A549	lung:	n/a	n/a
9	YY1	chr9:97807779-97808429	A549	lung:	n/a	n/a
10	BCL3	chr9:97805869-97809192	A549	lung:	n/a	chr9:97807640-97807649
11	POLR2A	chr9:97806754-97807970	A549	lung:	n/a	n/a
12	REST	chr9:97807012-97807936	A549	lung:	n/a	chr9:97807375-97807382 chr9:97807547-97807560
13	POLR2A	chr9:97806627-97808676	A549	lung:	n/a	n/a
14	FOXA2	chr9:97806965-97807910	A549	lung:	n/a	n/a
15	POLR2A	chr9:97807663-97807809	SK-N-SH	brain:	n/a	n/a
16	MAX	chr9:97806741-97807803	A549	lung:	n/a	n/a
17	CTCF	chr9:97806804-97809298	A549	lung:	n/a	chr9:97808280-97808298 chr9:97807606-97807619 chr9:97807066-97807075 chr9:97807801-97807814 chr9:97807525-97807538
18	SP1	chr9:97807128-97808432	A549	lung:	n/a	n/a
19	BCL3	chr9:97806825-97808589	A549	lung:	n/a	chr9:97807640-97807649
20	POLR2A	chr9:97807777-97807899	A549	lung:	n/a	n/a
21	POLR2A	chr9:97806834-97807872	ECC-1	luminal epithelium:	n/a	n/a
22	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
23	POLR2A	chr9:97806891-97807991	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97805704..97807873-chr9:97845688..97847934,2	MCF-7	breast:
2	chr9:97772268..97775206-chr9:97807423..97809466,2	K562	blood:
3	chr9:97807151..97809032-chr9:97838332..97840072,2	MCF-7	breast:
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	chr9:97804181..97807973-chr9:97809683..97813710,4	K562	blood:
8	chr9:97806251..97809142-chr9:97810861..97813740,3	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000207563	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000207864	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1004373	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117370	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119512	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121760	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512253	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761366	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761368	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761369	0.82[EUR][1000 genomes]
rs10761372	0.80[ASN][1000 genomes]
rs10993427	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993467	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412488	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564234	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571894	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571895	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061800	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404305	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404456	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3802456	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858089	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4537362	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743979	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743980	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743981	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743982	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744423	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744424	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744425	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744426	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744428	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744430	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744431	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744432	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744436	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479588	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479591	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479592	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020709	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7022452	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043705	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048786	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048941	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851173	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7854831	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862156	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863291	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865144	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7873567	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs962229	0.81[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
rs7871218	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

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	chr9:97797000-97807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:97800000-97808600	Genic enhancers	Liver	Liver
9	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:97803000-97810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:97804000-97808800	Weak transcription	Fetal Kidney	kidney
12	chr9:97804000-97810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:97804200-97807800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:97804400-97810400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:97804400-97810800	Weak transcription	K562	blood
16	chr9:97804800-97808200	Strong transcription	NH-A	brain
17	chr9:97804800-97808200	Strong transcription	NHLF	lung
18	chr9:97805000-97810000	Weak transcription	Brain Anterior Caudate	brain
19	chr9:97805200-97808400	Genic enhancers	Fetal Intestine Small	intestine
20	chr9:97805200-97810400	Weak transcription	Brain Angular Gyrus	brain
21	chr9:97805400-97810600	Weak transcription	Small Intestine	intestine
22	chr9:97805600-97810800	Weak transcription	GM12878-XiMat	blood
23	chr9:97806000-97807800	Strong transcription	Adipose Nuclei	Adipose
24	chr9:97806000-97808000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:97806000-97808000	Enhancers	Right Atrium	heart
26	chr9:97806000-97808200	Genic enhancers	Fetal Stomach	stomach
27	chr9:97806000-97808400	Genic enhancers	Fetal Intestine Large	intestine
28	chr9:97806200-97807800	Genic enhancers	Placenta	Placenta
29	chr9:97806200-97808000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr9:97806200-97808000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
31	chr9:97806200-97808000	Genic enhancers	Osteobl	bone
32	chr9:97806200-97808200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:97806200-97808200	Transcr. at gene 5' and 3'	A549	lung
34	chr9:97806400-97808000	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:97806400-97810600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:97806600-97808000	Genic enhancers	Spleen	Spleen
37	chr9:97806600-97808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:97806600-97808200	Enhancers	Psoas Muscle	Psoas
39	chr9:97806600-97810400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:97806800-97808000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:97806800-97808200	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr9:97806800-97808200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:97806800-97808400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:97806800-97808400	Enhancers	Gastric	stomach
45	chr9:97807000-97807800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:97807000-97807800	Genic enhancers	Colonic Mucosa	Colon
47	chr9:97807000-97808000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:97807000-97808000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:97807000-97808200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:97807000-97808200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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