Variant report

Variant	rs17456102
Chromosome Location	chr14:35627995-35627996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35450376..35452323-chr14:35627573..35629639,2	K562	blood:
2	chr14:35625114..35628050-chr14:35869275..35871381,2	MCF-7	breast:
3	chr14:35590512..35592667-chr14:35626960..35629855,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP2R3C-2	chr14:35627110-35628305	NONHSAT036367

Variant related genes	Relation type
ENSG00000258704	Chromatin interaction
ENSG00000258790	Chromatin interaction
ENSG00000092020	Chromatin interaction
ENSG00000100890	Chromatin interaction
ENSG00000100883	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10138507	0.80[EUR][1000 genomes]
rs10438061	0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs17103097	0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs17103098	0.81[GIH][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs17457389	1.00[ASW][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs17457568	1.00[AFR][1000 genomes]
rs17458137	1.00[AFR][1000 genomes]
rs17458214	1.00[AFR][1000 genomes]
rs17458367	0.82[CEU][hapmap];1.00[AFR][1000 genomes]
rs17458562	1.00[AFR][1000 genomes]
rs17458715	1.00[AFR][1000 genomes]
rs17509929	1.00[MEX][hapmap]
rs17510813	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs17511093	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17513024	1.00[AFR][1000 genomes]
rs17535082	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17536892	1.00[ASW][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes]
rs17536948	1.00[ASW][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes]
rs17537213	1.00[AFR][1000 genomes]
rs17537248	1.00[AFR][1000 genomes]
rs17595975	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17597246	1.00[AFR][1000 genomes]
rs17597667	1.00[AFR][1000 genomes]
rs28446606	0.80[EUR][1000 genomes]
rs28472413	0.80[EUR][1000 genomes]
rs45530731	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs45573840	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6571711	1.00[AFR][1000 genomes]
rs7143518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7146216	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7147426	0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs7151763	1.00[AFR][1000 genomes]
rs7154558	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7155406	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7156874	1.00[AFR][1000 genomes]
rs7159008	0.84[EUR][1000 genomes]
rs7160592	0.84[EUR][1000 genomes]
rs8005196	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8014523	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8014945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8015119	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8017772	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8018072	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8021263	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv901615	chr14:35485748-35630175	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1046992	chr14:35527239-35724227	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv1051274	chr14:35529529-35724227	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1048823	chr14:35537281-35724892	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv542032	chr14:35537281-35724892	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv1040540	chr14:35537481-35724753	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv542033	chr14:35537481-35724753	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1042625	chr14:35546094-35680358	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv1050123	chr14:35546114-35724892	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv542034	chr14:35546114-35724892	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv1050700	chr14:35548276-35639084	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1043692	chr14:35548276-35720016	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
20	nsv1047992	chr14:35563220-35639084	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
21	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
22	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
23	nsv1053978	chr14:35571762-35639084	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv1040300	chr14:35602956-35643888	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv1046680	chr14:35608347-35665374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17456102	FAM177A1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35593000-35638200	Weak transcription	Fetal Brain Male	brain
2	chr14:35593000-35660400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:35593200-35635400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr14:35594400-35629000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr14:35603200-35663400	Weak transcription	Fetal Lung	lung
6	chr14:35604200-35628800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:35604200-35651400	Weak transcription	Esophagus	oesophagus
8	chr14:35604400-35642000	Weak transcription	Lung	lung
9	chr14:35604400-35651800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr14:35604400-35660200	Weak transcription	Aorta	Aorta
11	chr14:35604600-35667400	Weak transcription	Spleen	Spleen
12	chr14:35605600-35628000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:35607400-35628200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:35607400-35642800	Weak transcription	Left Ventricle	heart
15	chr14:35607400-35662000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr14:35607600-35661200	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:35612000-35659800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr14:35612200-35628200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr14:35612200-35641800	Weak transcription	Fetal Stomach	stomach
20	chr14:35613600-35628000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr14:35613600-35628200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr14:35613600-35635800	Weak transcription	Brain Substantia Nigra	brain
23	chr14:35614000-35629000	Weak transcription	K562	blood
24	chr14:35616600-35628000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr14:35619400-35628200	Weak transcription	Fetal Intestine Small	intestine
26	chr14:35619800-35628200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr14:35621000-35628200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr14:35622000-35629600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr14:35622000-35645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:35622600-35628200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:35624600-35628400	Weak transcription	Fetal Intestine Large	intestine
32	chr14:35625000-35645200	Weak transcription	Gastric	stomach
33	chr14:35625400-35628000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr14:35625400-35644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr14:35625600-35628000	Weak transcription	Fetal Thymus	thymus
36	chr14:35625600-35628200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr14:35625600-35628200	Weak transcription	NH-A	brain
38	chr14:35625600-35628200	Weak transcription	NHLF	lung
39	chr14:35625600-35630000	Weak transcription	Small Intestine	intestine
40	chr14:35625600-35633400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:35625600-35633400	Weak transcription	Liver	Liver
42	chr14:35625600-35637800	Weak transcription	Brain Anterior Caudate	brain
43	chr14:35625600-35643000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr14:35625600-35644600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr14:35625600-35645200	Weak transcription	Brain Hippocampus Middle	brain
46	chr14:35625600-35650000	Weak transcription	Psoas Muscle	Psoas
47	chr14:35625600-35662200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr14:35625600-35662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr14:35625800-35628000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:35625800-35628000	Weak transcription	Primary B cells from peripheral blood	blood

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