Variant report

Variant	rs17312134
Chromosome Location	chr6:5209832-5209833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5209168..5211266-chr6:5213691..5215244,2	K562	blood:
2	chr6:5203877..5206736-chr6:5207600..5210343,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10498666	0.92[YRI][hapmap]
rs1411337	0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1535298	0.80[JPT][hapmap]
rs17139778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17139809	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs17139811	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs17140092	0.91[LWK][hapmap]
rs1884977	0.83[ASN][1000 genomes]
rs1983982	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2145373	0.92[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2208362	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs2326584	0.85[JPT][hapmap]
rs2746225	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2746227	1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs2746228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2753241	1.00[ASN][1000 genomes]
rs2753242	1.00[ASN][1000 genomes]
rs2773288	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2773292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773297	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773315	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs2773325	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs384574	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs409993	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4141760	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs444607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs446312	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4481464	0.91[LWK][hapmap]
rs4499975	0.88[ASN][1000 genomes]
rs4502984	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530910	0.89[ASN][1000 genomes]
rs4607474	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs4610609	0.87[ASN][1000 genomes]
rs6908240	0.85[JPT][hapmap]
rs6921061	0.83[LWK][hapmap]
rs72813608	1.00[ASN][1000 genomes]
rs730594	0.92[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs730595	0.92[ASN][1000 genomes]
rs744405	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs744756	0.90[ASN][1000 genomes]
rs744757	0.90[ASN][1000 genomes]
rs7756479	0.80[JPT][hapmap]
rs7775335	0.88[ASN][1000 genomes]
rs9328292	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9328294	0.85[JPT][hapmap]
rs9405815	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9405817	0.89[ASN][1000 genomes]
rs9502285	0.82[ASN][1000 genomes]
rs9504357	0.98[ASN][1000 genomes]
rs9504374	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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	8 gene(s)	inside rSNPs	diseases
15	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	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
rs17312134	PRPF4	trans	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5176200-5239600	Weak transcription	Thymus	Thymus
2	chr6:5180200-5212200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:5182000-5213600	Weak transcription	Gastric	stomach
4	chr6:5189000-5213200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:5192800-5213000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:5193200-5212400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:5194000-5220800	Weak transcription	GM12878-XiMat	blood
8	chr6:5201600-5213400	Weak transcription	Fetal Brain Male	brain
9	chr6:5201800-5213400	Weak transcription	Fetal Brain Female	brain
10	chr6:5202000-5212800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:5202800-5213600	Weak transcription	Dnd41	blood
12	chr6:5203200-5210000	Enhancers	Fetal Stomach	stomach
13	chr6:5203600-5210400	Enhancers	Colon Smooth Muscle	Colon
14	chr6:5203800-5213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:5204400-5213000	Weak transcription	Hela-S3	cervix
16	chr6:5205600-5212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:5205600-5213000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:5205600-5213400	Weak transcription	Fetal Thymus	thymus
19	chr6:5205600-5218800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:5205600-5220000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:5205600-5223000	Weak transcription	Right Atrium	heart
22	chr6:5206200-5214800	Weak transcription	Esophagus	oesophagus
23	chr6:5206200-5215600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:5206200-5215600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:5206200-5246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:5206400-5212600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:5206400-5213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:5206400-5214000	Weak transcription	Spleen	Spleen
29	chr6:5206400-5219400	Weak transcription	HMEC	breast
30	chr6:5206600-5211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:5206600-5212400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:5206600-5212800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:5206600-5213000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:5206600-5213000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:5206600-5213200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:5206600-5213200	Weak transcription	Brain Germinal Matrix	brain
37	chr6:5206600-5213600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:5206600-5213600	Weak transcription	A549	lung
39	chr6:5206600-5213800	Weak transcription	Right Ventricle	heart
40	chr6:5206600-5214000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:5206600-5214000	Weak transcription	Lung	lung
42	chr6:5206600-5214200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:5206600-5214800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:5206600-5215800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:5206600-5216200	Weak transcription	Pancreas	Pancrea
46	chr6:5206600-5240800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:5206800-5211000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:5206800-5212400	Weak transcription	Fetal Intestine Large	intestine
49	chr6:5206800-5212600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:5206800-5212600	Weak transcription	Adipose Nuclei	Adipose

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