Variant report

Variant	rs6441990
Chromosome Location	chr3:46484261-46484262
allele	C/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	CTCF	chr3:46484155-46484333	SK-N-SH_RA	brain:	n/a	chr3:46484250-46484260
2	CTCF	chr3:46484133-46484383	HUVEC	blood vessel:	n/a	chr3:46484250-46484260
3	CTCF	chr3:46484180-46484330	NHLF	lung:	n/a	chr3:46484250-46484260
4	RAD21	chr3:46484107-46484376	A549	lung:	n/a	n/a
5	SMC3	chr3:46484083-46484440	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr3:46484079-46484415	HepG2	liver:	n/a	chr3:46484250-46484260
7	CTCF	chr3:46484096-46484347	A549	lung:	n/a	chr3:46484250-46484260
8	CTCF	chr3:46484200-46484350	AG09309	skin:	n/a	chr3:46484250-46484260
9	CTCF	chr3:46484180-46484330	Hela-S3	cervix:	n/a	chr3:46484250-46484260
10	CTCF	chr3:46484064-46484391	H1-hESC	embryonic stem cell:	n/a	chr3:46484250-46484260
11	CTCF	chr3:46484220-46484370	GM12866	blood:	n/a	chr3:46484250-46484260
12	RAD21	chr3:46484086-46484473	HepG2	liver:	n/a	n/a
13	CTCF	chr3:46484220-46484370	A549	lung:	n/a	chr3:46484250-46484260
14	CTCF	chr3:46484200-46484350	HepG2	liver:	n/a	chr3:46484250-46484260
15	CTCF	chr3:46484140-46484290	Hela-S3	cervix:	n/a	chr3:46484250-46484260
16	CTCF	chr3:46484180-46484330	GM12875	blood:	n/a	chr3:46484250-46484260
17	CTCF	chr3:46484160-46484310	HBMEC	blood vessel:	n/a	chr3:46484250-46484260
18	CTCF	chr3:46484180-46484330	AG09309	skin:	n/a	chr3:46484250-46484260
19	CTCF	chr3:46484180-46484330	GM12871	blood:	n/a	chr3:46484250-46484260
20	YY1	chr3:46484172-46484344	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:46484162-46484355	LNCaP	prostate:	n/a	chr3:46484250-46484260
22	RAD21	chr3:46483909-46484627	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr3:46484160-46484310	HA-sp	spinal cord:	n/a	chr3:46484250-46484260
24	RAD21	chr3:46484078-46484460	MCF-7	breast:	n/a	n/a
25	CTCF	chr3:46484220-46484370	GM12875	blood:	n/a	chr3:46484250-46484260
26	CTCF	chr3:46484200-46484350	HA-sp	spinal cord:	n/a	chr3:46484250-46484260
27	CTCF	chr3:46484153-46484376	GM13977	blood:	n/a	chr3:46484250-46484260
28	RAD21	chr3:46484129-46484375	HepG2	liver:	n/a	n/a
29	CTCF	chr3:46484180-46484330	SK-N-SH_RA	brain:	n/a	chr3:46484250-46484260
30	CTCF	chr3:46484200-46484350	AoAF	blood vessel:	n/a	chr3:46484250-46484260
31	CTCF	chr3:46484177-46484407	GM19239	blood:	n/a	chr3:46484250-46484260
32	CTCF	chr3:46484160-46484310	GM12871	blood:	n/a	chr3:46484250-46484260
33	CTCF	chr3:46484155-46484418	A549	lung:	n/a	chr3:46484250-46484260
34	CTCF	chr3:46483869-46484624	A549	lung:	n/a	chr3:46484250-46484260
35	CTCF	chr3:46484160-46484310	HMF	breast:	n/a	chr3:46484250-46484260
36	RAD21	chr3:46484112-46484359	SK-N-SH_RA	brain:	n/a	n/a
37	RAD21	chr3:46483971-46484515	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:46484155-46484384	GM10248	blood:	n/a	chr3:46484250-46484260
39	RAD21	chr3:46484073-46484463	MCF-7	breast:	n/a	n/a
40	CTCF	chr3:46484168-46484340	Pancreas_OC	pancreas:	n/a	chr3:46484250-46484260
41	CTCF	chr3:46484160-46484310	HAc	cerebellar:	n/a	chr3:46484250-46484260
42	CTCF	chr3:46484219-46484377	MCF-7	breast:	n/a	chr3:46484250-46484260
43	RAD21	chr3:46483976-46484489	A549	lung:	n/a	n/a
44	CTCF	chr3:46484180-46484330	HCFaa	heart:	n/a	chr3:46484250-46484260
45	CTCF	chr3:46484180-46484330	BE2_C	brain:	n/a	chr3:46484250-46484260
46	MAX	chr3:46483877-46484342	NB4	blood:	n/a	chr3:46484005-46484015 chr3:46484035-46484045
47	CTCF	chr3:46483993-46484401	A549	lung:	n/a	chr3:46484250-46484260
48	CTCF	chr3:46484159-46484386	GM20000	blood:	n/a	chr3:46484250-46484260
49	CTCF	chr3:46484154-46484321	HepG2	liver:	n/a	chr3:46484250-46484260
50	RAD21	chr3:46484034-46484502	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46436027..46436544-chr3:46483822..46484338,2	MCF-7	breast:
2	chr3:46479732..46482447-chr3:46484213..46487607,4	K562	blood:
3	chr3:46484040..46488296-chr3:46490659..46494329,4	MCF-7	breast:
4	chr3:46436690..46437276-chr3:46483787..46484399,2	MCF-7	breast:

Variant related genes	Relation type
LTF	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1042073	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs11130091	0.80[CEU][hapmap]
rs1126478	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs11707471	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs11716497	1.00[CEU][hapmap]
rs4234463	1.00[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs4683234	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs6441992	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs6441995	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs6776504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6794622	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs743659	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9862186	0.81[CEU][hapmap]
rs9862388	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap]

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	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46455800-46496800	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:46459400-46491600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:46465200-46488800	Weak transcription	Left Ventricle	heart
4	chr3:46465200-46488800	Weak transcription	Right Ventricle	heart
5	chr3:46479600-46485000	Enhancers	Primary T cells from cord blood	blood
6	chr3:46479600-46487000	Enhancers	Fetal Thymus	thymus
7	chr3:46479800-46485000	Enhancers	Dnd41	blood
8	chr3:46480200-46504000	Weak transcription	Lung	lung
9	chr3:46481000-46488800	Strong transcription	Spleen	Spleen
10	chr3:46481200-46485800	Weak transcription	Gastric	stomach
11	chr3:46482200-46485000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:46482200-46485000	Enhancers	Fetal Brain Male	brain
13	chr3:46482400-46485200	Enhancers	Fetal Lung	lung
14	chr3:46483000-46486800	Weak transcription	Pancreas	Pancrea
15	chr3:46483000-46488600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:46483400-46484400	Weak transcription	Fetal Stomach	stomach
17	chr3:46483400-46486800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:46484000-46485000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:46484200-46484800	Enhancers	Fetal Intestine Small	intestine

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