Variant report

Variant	rs35219849
Chromosome Location	chr3:50243801-50243802
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	FOXA1	chr3:50243299-50243824	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:50242313-50243876	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:50243391-50243861	HepG2	liver:	n/a	n/a
4	MAX	chr3:50242124-50243975	HepG2	liver:	n/a	chr3:50243602-50243612 chr3:50243430-50243440
5	MAX	chr3:50243196-50243901	HepG2	liver:	n/a	chr3:50243602-50243612 chr3:50243430-50243440
6	RCOR1	chr3:50243511-50243863	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:50243231-50244015	HepG2	liver:	n/a	n/a
8	MXI1	chr3:50243303-50243941	HepG2	liver:	n/a	n/a
9	FOXA1	chr3:50243297-50243829	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:50241959-50243890	HepG2	liver:	n/a	n/a
11	FOXA1	chr3:50243420-50243851	HepG2	liver:	n/a	n/a
12	MAZ	chr3:50243440-50243806	HepG2	liver:	n/a	chr3:50243602-50243612
13	HEY1	chr3:50243165-50243953	HepG2	liver:	n/a	n/a
14	MAX	chr3:50242508-50243973	HCT-116	colon:	n/a	chr3:50243602-50243612 chr3:50243430-50243440
15	MAX	chr3:50242671-50243836	ECC-1	luminal epithelium:	n/a	chr3:50243602-50243612 chr3:50243430-50243440
16	MAX	chr3:50243192-50243896	ECC-1	luminal epithelium:	n/a	chr3:50243602-50243612 chr3:50243430-50243440
17	SP1	chr3:50243344-50243871	HepG2	liver:	n/a	chr3:50243537-50243549 chr3:50243537-50243549 chr3:50243539-50243548 chr3:50243538-50243547 chr3:50243554-50243575

No.	Distal block	Cell Line	Cell type
1	chr3:50226233..50229498-chr3:50242660..50245494,3	K562	blood:
2	chr3:50239764..50242755-chr3:50243671..50247708,3	K562	blood:
3	chr3:50242260..50244177-chr3:50332568..50334684,2	K562	blood:
4	chr3:50242278..50244597-chr3:50304376..50306670,2	K562	blood:
5	chr3:50243330..50243871-chr6:52024604..52025477,2	MCF-7	breast:

Variant related genes	Relation type
SLC38A3	TF binding region
ENSG00000012171	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000114349	Chromatin interaction
ENSG00000188338	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1046956	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11919418	0.90[EUR][1000 genomes]
rs12632110	0.85[EUR][1000 genomes]
rs12637671	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13059311	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13064381	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13067082	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs14321	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2236940	0.94[EUR][1000 genomes]
rs2236941	0.94[EUR][1000 genomes]
rs2526384	0.82[EUR][1000 genomes]
rs2624833	0.86[EUR][1000 genomes]
rs2624835	0.86[EUR][1000 genomes]
rs2624838	0.82[EUR][1000 genomes]
rs2624841	0.86[EUR][1000 genomes]
rs35137368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58648044	0.94[EUR][1000 genomes]
rs6807194	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9858297	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
3	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
10	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
11	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription 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	99 gene(s)	inside rSNPs	diseases
14	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
15	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases
16	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
20	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
24	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
25	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
26	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
28	nsv876771	chr3:50225568-50247824	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
29	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35219849	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs35219849	HYAL3	cis	Esophagus Muscularis	GTEx
rs35219849	RBM6	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50242200-50244400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:50242400-50244000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:50242400-50244200	Active TSS	Brain Hippocampus Middle	brain
4	chr3:50242600-50244000	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr3:50242800-50244000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:50243200-50244000	Bivalent Enhancer	Primary T cells from cord blood	blood
7	chr3:50243200-50244000	Bivalent Enhancer	Placenta	Placenta
8	chr3:50243200-50244000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr3:50243400-50244000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:50243400-50244000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:50243400-50244000	Bivalent Enhancer	Esophagus	oesophagus
12	chr3:50243400-50244200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
13	chr3:50243400-50244400	Enhancers	Fetal Heart	heart
14	chr3:50243400-50245800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr3:50243600-50244000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr3:50243600-50244000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr3:50243600-50244000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr3:50243600-50244000	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr3:50243600-50244000	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr3:50243600-50244000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr3:50243600-50244000	Bivalent Enhancer	Fetal Stomach	stomach
22	chr3:50243600-50244000	Flanking Active TSS	Pancreas	Pancrea
23	chr3:50243600-50244000	Enhancers	Right Atrium	heart
24	chr3:50243600-50244200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:50243600-50244400	Enhancers	Right Ventricle	heart
26	chr3:50243600-50244400	Transcr. at gene 5' and 3'	HepG2	liver
27	chr3:50243600-50245000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:50243600-50245200	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr3:50243600-50245600	Flanking Active TSS	Liver	Liver
30	chr3:50243600-50245800	Enhancers	Psoas Muscle	Psoas
31	chr3:50243600-50246000	Weak transcription	Ovary	ovary
32	chr3:50243800-50244000	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:50243800-50244000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr3:50243800-50244000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr3:50243800-50244000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:50243800-50244200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:50243800-50244200	Enhancers	Left Ventricle	heart
38	chr3:50243800-50244400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:50243800-50244600	Enhancers	Brain Angular Gyrus	brain
40	chr3:50243800-50246400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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