Variant report

Variant	rs9659310
Chromosome Location	chr1:246014673-246014674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:245912433..245914133-chr1:246013964..246015796,2	K562	blood:
2	chr1:246014320..246017161-chr1:246018009..246019669,2	K562	blood:
3	chr1:246009381..246012299-chr1:246014138..246015859,2	MCF-7	breast:
4	chr1:246010644..246013131-chr1:246014185..246016715,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10754480	0.82[JPT][hapmap]
rs10924361	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924362	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048995	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12750832	0.87[JPT][hapmap]
rs2885547	0.86[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73140710	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9287180	0.88[JPT][hapmap]
rs9659982	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9662149	0.86[EUR][1000 genomes]
rs9662165	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9662617	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1011255	chr1:245913512-246065050	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv998801	chr1:245924108-246131115	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv535386	chr1:245924108-246131115	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1014841	chr1:245936464-246143222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv535387	chr1:245936464-246143222	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1008786	chr1:245948622-246514454	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv535388	chr1:245948622-246514454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv468805	chr1:245950642-246229245	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv549521	chr1:245950642-246229245	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv873405	chr1:245959911-246093644	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1001290	chr1:245966190-246018587	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv535391	chr1:245966190-246018587	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
23	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
25	nsv873406	chr1:245991027-246039231	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv1005074	chr1:245999762-246141613	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv1013699	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	nsv535393	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9659310	ESF1	trans	brain	seeQTL
rs9659310	NUFIP2	trans	brain	seeQTL
rs9659310	NFIC	trans	brain	seeQTL
rs9659310	DYNC1LI2	trans	brain	seeQTL
rs9659310	ARID4B	trans	brain	seeQTL
rs9659310	ARAP2	trans	brain	seeQTL
rs9659310	NAPG	trans	brain	seeQTL
rs9659310	TMEM5	trans	brain	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245974400-246020800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:245986600-246021600	Weak transcription	Fetal Stomach	stomach
3	chr1:245987000-246015000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:245990800-246016600	Weak transcription	Lung	lung
5	chr1:245990800-246019000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:245991000-246018000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:245991000-246045000	Weak transcription	Spleen	Spleen
8	chr1:245991200-246019200	Weak transcription	Pancreas	Pancrea
9	chr1:245994400-246018000	Weak transcription	HepG2	liver
10	chr1:245996800-246021200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:245997000-246015200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:245997600-246023800	Weak transcription	Ovary	ovary
13	chr1:245998000-246020400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:245998200-246020800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:245998400-246017600	Weak transcription	Primary B cells from cord blood	blood
16	chr1:245999400-246019200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:245999400-246024200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:245999800-246038400	Weak transcription	Aorta	Aorta
19	chr1:246000200-246019200	Weak transcription	Gastric	stomach
20	chr1:246000200-246019200	Weak transcription	NHLF	lung
21	chr1:246000800-246019200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:246001200-246023400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:246001800-246015000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:246001800-246016200	Weak transcription	Osteobl	bone
25	chr1:246001800-246016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:246001800-246019200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:246001800-246019200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:246001800-246056800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:246006600-246021800	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:246006800-246041200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:246007000-246019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:246007200-246015000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:246007600-246019600	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:246007800-246019400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:246009000-246015000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:246009600-246038200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:246010200-246019200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:246010200-246028200	Weak transcription	Thymus	Thymus
39	chr1:246011000-246017800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:246011800-246015200	Weak transcription	Left Ventricle	heart
41	chr1:246012000-246016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:246012000-246024800	Weak transcription	Esophagus	oesophagus
43	chr1:246012600-246021800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr1:246012800-246021200	Weak transcription	Dnd41	blood
45	chr1:246012800-246049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:246013200-246023200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:246013800-246020400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:246014000-246014800	Weak transcription	K562	blood
49	chr1:246014000-246022000	Strong transcription	Primary T cells from cord blood	blood
50	chr1:246014200-246026400	Weak transcription	Brain Anterior Caudate	brain

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