Variant report

Variant	rs9866958
Chromosome Location	chr3:142338441-142338442
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	MYC	chr3:142337975-142338652	MCF10A-Er-Src	breast:	n/a	chr3:142338158-142338167
2	JUND	chr3:142337937-142338466	HCT-116	colon:	n/a	chr3:142338156-142338168 chr3:142338156-142338167 chr3:142338157-142338166
3	FOSL2	chr3:142337614-142338605	A549	lung:	n/a	chr3:142338156-142338168 chr3:142338157-142338166
4	MAX	chr3:142337551-142338475	A549	lung:	n/a	chr3:142338158-142338167
5	JUN	chr3:142337456-142338463	K562	blood:	n/a	chr3:142338156-142338168 chr3:142338157-142338166
6	SP1	chr3:142337816-142338462	A549	lung:	n/a	n/a
7	CTCF	chr3:142338441-142338486	K562	blood:	n/a	n/a
8	TCF12	chr3:142337700-142338576	A549	lung:	n/a	chr3:142338191-142338198
9	JUND	chr3:142337629-142338461	K562	blood:	n/a	chr3:142338156-142338168 chr3:142338156-142338167 chr3:142338157-142338166
10	SP1	chr3:142337855-142338478	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142337305..142339939-chr3:142351079..142353328,2	K562	blood:
2	chr3:142336507..142339486-chr3:142355322..142357574,2	MCF-7	breast:
3	chr3:142338028..142339583-chr3:142381758..142384613,2	MCF-7	breast:
4	chr3:142336924..142339246-chr3:142443118..142445487,2	MCF-7	breast:

Variant related genes	Relation type
PLS1	TF binding region
ENSG00000144935	Chromatin interaction
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10935465	0.85[EUR][1000 genomes]
rs1129393	0.85[EUR][1000 genomes]
rs11715610	0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12695767	0.80[ASN][1000 genomes]
rs12695768	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13058771	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13065075	0.81[EUR][1000 genomes]
rs13067795	0.83[EUR][1000 genomes]
rs13069113	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13069307	0.81[EUR][1000 genomes]
rs13079246	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13080785	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13085998	0.84[EUR][1000 genomes]
rs13093869	0.92[EUR][1000 genomes]
rs13100985	0.82[ASN][1000 genomes]
rs1357529	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1357530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16852486	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs17623267	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1916639	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1983434	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983435	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2012010	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2030613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049325	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2049326	0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2140432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2177396	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227928	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2227930	0.85[EUR][1000 genomes]
rs2354175	0.84[ASN][1000 genomes]
rs2354860	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2883380	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3736560	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3736561	0.82[ASN][1000 genomes]
rs3922730	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs4413348	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683688	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4683689	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4683690	0.88[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4683691	0.81[AMR][1000 genomes]
rs6414350	0.82[EUR][1000 genomes]
rs6440088	0.85[EUR][1000 genomes]
rs6440089	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs6440090	0.90[EUR][1000 genomes]
rs6440091	0.88[EUR][1000 genomes]
rs6440092	0.90[EUR][1000 genomes]
rs6440093	0.91[EUR][1000 genomes]
rs6440094	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs6440098	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440099	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440102	0.86[AMR][1000 genomes]
rs6768093	0.86[EUR][1000 genomes]
rs6770155	0.90[EUR][1000 genomes]
rs6775813	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6780250	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs6782400	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs6783203	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6784089	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6784361	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6785894	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6789958	0.88[CEU][hapmap]
rs6792259	0.92[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6793735	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6798232	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6799752	0.92[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs6802734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6802774	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6808205	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs6808302	0.82[ASN][1000 genomes]
rs7428496	0.87[EUR][1000 genomes]
rs7430429	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7609842	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610557	0.92[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs7615316	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631313	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7635146	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7641330	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7646880	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7647573	0.84[EUR][1000 genomes]
rs7648354	0.94[CHB][hapmap];0.82[AMR][1000 genomes]
rs7651071	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs7651542	0.83[EUR][1000 genomes]
rs940211	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs940212	0.84[ASN][1000 genomes]
rs9683085	0.84[EUR][1000 genomes]
rs9816736	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs9824176	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824893	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9825207	0.86[EUR][1000 genomes]
rs9832606	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9846960	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs9862919	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9869842	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs9879995	0.86[EUR][1000 genomes]
rs9882763	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142334000-142357200	Weak transcription	Pancreas	Pancrea
2	chr3:142336000-142339400	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr3:142336000-142340800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr3:142337200-142338800	Flanking Active TSS	A549	lung
5	chr3:142337400-142338600	Enhancers	HUVEC	blood vessel
6	chr3:142337600-142338600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:142337600-142338600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:142337600-142338600	Enhancers	Hela-S3	cervix
9	chr3:142337600-142338600	Enhancers	HMEC	breast
10	chr3:142337600-142339000	Enhancers	NHEK	skin
11	chr3:142337600-142340600	Weak transcription	Small Intestine	intestine
12	chr3:142337800-142348400	Weak transcription	Gastric	stomach
13	chr3:142338000-142339800	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr3:142338000-142340600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:142338000-142340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:142338000-142340800	Enhancers	Stomach Mucosa	stomach
17	chr3:142338000-142344200	Weak transcription	Colonic Mucosa	Colon
18	chr3:142338200-142339000	Enhancers	K562	blood
19	chr3:142338400-142338600	Enhancers	HSMMtube	muscle
20	chr3:142338400-142339400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:142338400-142340600	Weak transcription	Fetal Intestine Small	intestine
22	chr3:142338400-142341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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