Variant report

Variant	rs6762327
Chromosome Location	chr3:194931797-194931798
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	TCF12	chr3:194930437-194931947	SK-N-SH	brain:	n/a	chr3:194931446-194931453 chr3:194931206-194931213
2	NFIC	chr3:194930638-194931799	SK-N-SH	brain:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
3	TCF12	chr3:194930532-194931905	SK-N-SH	brain:	n/a	chr3:194931446-194931453 chr3:194931206-194931213
4	NFIC	chr3:194930487-194931928	SK-N-SH	brain:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
5	MEF2A	chr3:194930955-194931870	SK-N-SH	brain:	n/a	chr3:194931386-194931407 chr3:194931388-194931403 chr3:194931388-194931402 chr3:194931390-194931401 chr3:194931386-194931407 chr3:194931386-194931407 chr3:194931387-194931404 chr3:194931391-194931400 chr3:194931387-194931403
6	PBX3	chr3:194930723-194931880	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr3:194930965-194931832	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:194931000-194931801	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr3:194930868-194931943	SK-N-SH	brain:	n/a	chr3:194931823-194931834

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194931478..194933050-chr3:194933815..194935477,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-25P	TF binding region
XXYLT1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs56835677	0.92[AFR][1000 genomes]
rs59806212	1.00[AMR][1000 genomes]
rs6771779	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
10	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
11	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
12	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
18	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194918800-194945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:194919400-194945200	Weak transcription	Thymus	Thymus
3	chr3:194921000-194941600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:194924600-194931800	Enhancers	Placenta	Placenta
5	chr3:194926400-194942600	Weak transcription	Small Intestine	intestine
6	chr3:194926400-194947600	Weak transcription	Gastric	stomach
7	chr3:194926600-194933400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:194926600-194942800	Weak transcription	Hela-S3	cervix
9	chr3:194927600-194931800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:194927800-194931800	Enhancers	Fetal Thymus	thymus
11	chr3:194928400-194931800	Enhancers	Left Ventricle	heart
12	chr3:194928400-194932000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:194928400-194932000	Enhancers	Brain Germinal Matrix	brain
14	chr3:194928400-194932600	Enhancers	Ovary	ovary
15	chr3:194928400-194932600	Enhancers	NHLF	lung
16	chr3:194928600-194931800	Enhancers	Right Ventricle	heart
17	chr3:194928600-194932200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:194928600-194932400	Enhancers	Fetal Heart	heart
19	chr3:194928600-194932600	Enhancers	Fetal Stomach	stomach
20	chr3:194928600-194933600	Enhancers	Lung	lung
21	chr3:194928800-194931800	Enhancers	Brain Hippocampus Middle	brain
22	chr3:194929000-194931800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:194929000-194931800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:194929000-194931800	Enhancers	K562	blood
25	chr3:194929000-194932400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:194929200-194932400	Enhancers	HUVEC	blood vessel
27	chr3:194929400-194931800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:194929400-194932000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:194929400-194932400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:194929400-194932600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:194929600-194931800	Enhancers	Right Atrium	heart
32	chr3:194929600-194932400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:194929800-194947400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:194930400-194931800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:194930400-194932000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:194930600-194931800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:194930600-194931800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:194930600-194931800	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:194930600-194931800	Enhancers	Pancreas	Pancrea
40	chr3:194930600-194932600	Enhancers	Fetal Muscle Trunk	muscle
41	chr3:194930800-194931800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:194930800-194931800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:194930800-194931800	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:194930800-194932200	Enhancers	Stomach Mucosa	stomach
45	chr3:194931000-194931800	Enhancers	A549	lung
46	chr3:194931000-194931800	Flanking Active TSS	Osteobl	bone
47	chr3:194931200-194931800	Enhancers	Rectal Smooth Muscle	rectum
48	chr3:194931200-194932000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:194931200-194932000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:194931200-194932200	Enhancers	Fetal Lung	lung

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