Variant report

Variant	rs6994734
Chromosome Location	chr8:6269442-6269443
allele	G/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	WRNIP1	chr8:6269349-6269543	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:6261231..6262782-chr8:6268049..6270486,2	K562	blood:
2	chr8:6262086..6265734-chr8:6266423..6270611,6	MCF-7	breast:
3	chr8:6269409..6272361-chr8:6283113..6285800,2	K562	blood:

Variant related genes	Relation type
ENSG00000246089	TF binding region
ENSG00000246089	Chromatin interaction
ENSG00000147316	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11137033	0.84[JPT][hapmap]
rs1129704	0.82[CHB][hapmap]
rs12674488	0.84[JPT][hapmap]
rs12677501	0.84[JPT][hapmap]
rs13267816	0.84[JPT][hapmap]
rs1530408	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs1530409	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs1550697	0.84[ASW][hapmap];0.84[GIH][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs1550698	0.91[AFR][1000 genomes]
rs17077109	0.84[JPT][hapmap]
rs1867385	0.82[CHB][hapmap]
rs1966818	0.90[JPT][hapmap]
rs2034143	0.82[CHB][hapmap]
rs2120483	0.84[AFR][1000 genomes]
rs2305022	0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs2440412	0.82[CHB][hapmap]
rs2440413	0.82[CHB][hapmap]
rs2440422	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2440427	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2440428	0.84[JPT][hapmap]
rs2440443	0.92[ASN][1000 genomes]
rs2442491	0.82[JPT][hapmap]
rs2442516	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2442517	0.84[JPT][hapmap]
rs2442521	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs2442523	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2442524	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2442533	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2442536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs2442546	0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2515555	0.95[JPT][hapmap]
rs2515564	0.89[JPT][hapmap]
rs2515565	0.90[JPT][hapmap]
rs2515572	0.82[CHB][hapmap]
rs2920665	0.84[JPT][hapmap]
rs2920677	0.83[JPT][hapmap]
rs2920689	0.84[JPT][hapmap]
rs2922811	0.84[JPT][hapmap]
rs2922813	0.84[JPT][hapmap]
rs2922814	0.81[GIH][hapmap];0.84[JPT][hapmap]
rs2922815	0.84[JPT][hapmap]
rs60526807	0.89[AFR][1000 genomes]
rs61048567	0.94[ASN][1000 genomes]
rs6559160	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6559161	0.84[JPT][hapmap]
rs6995735	0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7002495	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7002509	0.94[JPT][hapmap]
rs7008037	0.90[JPT][hapmap]
rs7008227	0.95[JPT][hapmap]
rs7009134	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs894888	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs930557	0.82[CHB][hapmap]
rs963754	0.82[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1018782	chr8:5984032-6284373	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	7 gene(s)	inside rSNPs	diseases
4	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv949501	chr8:6081704-6303511	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv890041	chr8:6084048-6274963	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1024103	chr8:6124125-6303511	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1026950	chr8:6127991-6303511	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1025734	chr8:6128828-6303511	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1022940	chr8:6128828-6304814	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv527005	chr8:6129051-6287170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS 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	6 gene(s)	inside rSNPs	diseases
14	nsv1028552	chr8:6129221-6303511	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1021800	chr8:6144798-6286635	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1026004	chr8:6144798-6307692	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv539431	chr8:6144798-6307692	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv933107	chr8:6173244-6312807	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1018882	chr8:6204857-6289937	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv531468	chr8:6248682-6309194	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1033935	chr8:6262180-6275753	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv524404	chr8:6263083-6291485	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	nsv1030323	chr8:6268228-6279511	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6994734	MCPH1	Cis_1M	lymphoblastoid	RTeQTL
rs6994734	AGPAT5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6272600	Weak transcription	Esophagus	oesophagus
2	chr8:6265000-6272600	Weak transcription	Gastric	stomach
3	chr8:6265000-6286600	Weak transcription	Small Intestine	intestine
4	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr8:6265200-6269600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:6265200-6269600	Weak transcription	Pancreas	Pancrea
7	chr8:6265200-6281800	Weak transcription	Right Atrium	heart
8	chr8:6265200-6281800	Weak transcription	Right Ventricle	heart
9	chr8:6265200-6282600	Weak transcription	Colonic Mucosa	Colon
10	chr8:6265200-6302200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr8:6265400-6269600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:6265400-6270000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr8:6265400-6272600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr8:6265400-6278200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr8:6265400-6287400	Weak transcription	Psoas Muscle	Psoas
16	chr8:6265400-6303800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:6265600-6276400	Weak transcription	Fetal Brain Male	brain
18	chr8:6265600-6290000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:6266000-6275800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:6266000-6275800	Strong transcription	Fetal Muscle Leg	muscle
21	chr8:6266200-6270400	Strong transcription	Fetal Stomach	stomach
22	chr8:6266600-6269600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr8:6266600-6269600	Strong transcription	Left Ventricle	heart
24	chr8:6266600-6269800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr8:6266600-6269800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr8:6266600-6269800	Strong transcription	HUVEC	blood vessel
27	chr8:6266600-6270400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr8:6266600-6270400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr8:6266600-6270600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr8:6266600-6270600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr8:6266600-6270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:6266600-6271000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr8:6266600-6271000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:6266600-6271000	Strong transcription	Fetal Intestine Large	intestine
35	chr8:6266600-6271000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr8:6266600-6271200	Strong transcription	Fetal Thymus	thymus
37	chr8:6266600-6275200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:6266800-6269600	Strong transcription	HSMM	muscle
39	chr8:6266800-6269800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr8:6266800-6269800	Strong transcription	Liver	Liver
41	chr8:6266800-6269800	Strong transcription	Ovary	ovary
42	chr8:6266800-6269800	Strong transcription	Osteobl	bone
43	chr8:6266800-6270000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr8:6266800-6270400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr8:6266800-6270600	Strong transcription	A549	lung
46	chr8:6266800-6271000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr8:6266800-6271000	Strong transcription	Brain Anterior Caudate	brain
48	chr8:6266800-6271400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr8:6266800-6272800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr8:6266800-6273400	Strong transcription	Monocytes-CD14+_RO01746	blood

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