Variant report

Variant	rs2920674
Chromosome Location	chr8:6347120-6347121
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:6340740..6343384-chr8:6345418..6348031,2	K562	blood:
2	chr8:6340740..6344062-chr8:6345418..6348031,3	K562	blood:

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1031309	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1054073	0.94[JPT][hapmap]
rs11137029	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs11137033	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1129703	0.88[JPT][hapmap]
rs1129704	0.83[JPT][hapmap]
rs1129706	0.94[JPT][hapmap]
rs12546890	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs12550299	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs12674488	0.81[CEU][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs12675930	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs12676907	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs12676922	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs12677501	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs12679619	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12680048	0.98[ASN][1000 genomes]
rs12681009	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13248420	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13267816	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs13281793	0.80[ASN][1000 genomes]
rs13281967	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs13282022	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs13282116	0.80[ASN][1000 genomes]
rs13282577	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs1373307	0.83[JPT][hapmap]
rs1550690	1.00[JPT][hapmap]
rs17077056	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs17077067	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs17077083	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs17077094	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17077109	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs17613024	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1867385	0.88[JPT][hapmap]
rs1867386	0.94[JPT][hapmap]
rs1868551	0.94[JPT][hapmap]
rs1868555	0.92[ASN][1000 genomes]
rs2034143	0.88[JPT][hapmap]
rs2251956	0.83[JPT][hapmap]
rs2254903	0.88[JPT][hapmap]
rs2277136	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs2305022	0.84[JPT][hapmap]
rs2440392	0.94[CEU][hapmap];0.85[ASN][1000 genomes]
rs2440396	0.81[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2440397	0.92[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2440399	0.82[CEU][hapmap]
rs2440401	0.88[CEU][hapmap]
rs2440406	1.00[JPT][hapmap]
rs2440412	0.83[JPT][hapmap]
rs2440414	0.94[JPT][hapmap]
rs2440416	1.00[JPT][hapmap]
rs2440423	0.83[JPT][hapmap]
rs2440424	0.88[JPT][hapmap]
rs2440428	0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2440430	0.84[CHB][hapmap]
rs2440432	1.00[JPT][hapmap]
rs2442483	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442485	1.00[JPT][hapmap]
rs2442491	0.81[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2442492	0.82[CEU][hapmap]
rs2442493	0.92[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2442496	0.82[CEU][hapmap]
rs2442497	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs2442500	0.91[CEU][hapmap]
rs2442502	0.88[JPT][hapmap]
rs2442510	0.94[JPT][hapmap]
rs2442511	1.00[JPT][hapmap]
rs2442517	0.83[JPT][hapmap]
rs2442518	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs2442522	0.83[JPT][hapmap]
rs2442523	0.83[JPT][hapmap]
rs2442524	0.89[JPT][hapmap]
rs2515572	0.88[JPT][hapmap]
rs2515574	0.85[CHB][hapmap]
rs2515582	0.85[CEU][hapmap]
rs2515583	0.88[CEU][hapmap]
rs2515585	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2916733	0.94[CEU][hapmap]
rs2916734	0.88[CEU][hapmap]
rs2916737	0.94[CEU][hapmap]
rs2916738	0.94[CEU][hapmap]
rs2916740	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2916741	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2916742	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2916743	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2916746	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2916750	0.94[JPT][hapmap]
rs2920658	0.94[CEU][hapmap]
rs2920659	0.94[JPT][hapmap]
rs2920660	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2920671	0.89[JPT][hapmap]
rs2920677	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2920678	0.93[ASN][1000 genomes]
rs2920681	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2920689	0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2922811	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2922813	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2922814	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2922815	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2922818	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2922820	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2979648	0.94[JPT][hapmap]
rs2979652	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2979655	0.82[CEU][hapmap]
rs2979664	0.93[ASN][1000 genomes]
rs3020270	0.94[JPT][hapmap]
rs3020281	0.88[CEU][hapmap]
rs3020289	0.87[ASN][1000 genomes]
rs34009442	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34635086	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34748476	0.83[ASN][1000 genomes]
rs35150903	0.83[ASN][1000 genomes]
rs35248379	0.87[ASN][1000 genomes]
rs57804372	0.87[ASN][1000 genomes]
rs58679306	0.92[ASN][1000 genomes]
rs6559162	0.83[JPT][hapmap]
rs6559164	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs6989935	0.81[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6995735	0.84[JPT][hapmap]
rs7002187	0.88[JPT][hapmap]
rs7002509	0.87[JPT][hapmap]
rs73520657	0.94[ASN][1000 genomes]
rs7824209	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs7833481	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs894895	0.88[JPT][hapmap]
rs930557	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1025860	chr8:6328628-6360743	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv890058	chr8:6329510-6367302	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920674	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
2	chr8:6308000-6372600	Weak transcription	HMEC	breast
3	chr8:6317800-6380200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr8:6325800-6374400	Weak transcription	K562	blood
5	chr8:6336800-6377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:6337800-6347600	Strong transcription	Primary T cells from cord blood	blood
7	chr8:6338800-6347600	Strong transcription	Fetal Thymus	thymus
8	chr8:6338800-6360400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:6338800-6360600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:6338800-6369600	Weak transcription	Spleen	Spleen
11	chr8:6338800-6389600	Weak transcription	HSMMtube	muscle
12	chr8:6339800-6360400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr8:6340000-6360400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr8:6340400-6347600	Weak transcription	HepG2	liver
15	chr8:6340400-6371600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr8:6340800-6355400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr8:6340800-6360200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:6340800-6360400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr8:6340800-6371800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:6341000-6347600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr8:6341000-6360200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr8:6341000-6360600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr8:6341000-6372000	Weak transcription	A549	lung
24	chr8:6341000-6375000	Weak transcription	Brain Angular Gyrus	brain
25	chr8:6341200-6348200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr8:6341200-6354800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr8:6341200-6360400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr8:6341200-6360400	Weak transcription	Fetal Muscle Leg	muscle
29	chr8:6341200-6360800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr8:6341200-6369400	Weak transcription	Primary B cells from cord blood	blood
31	chr8:6341200-6371200	Weak transcription	Fetal Brain Female	brain
32	chr8:6341400-6347400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr8:6341400-6363600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:6341800-6360600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr8:6342000-6360400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr8:6342200-6352200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr8:6342400-6350400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:6342400-6355600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr8:6342400-6357600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr8:6342400-6359200	Weak transcription	Left Ventricle	heart
41	chr8:6342400-6360200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:6342400-6360200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr8:6342400-6360200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr8:6342400-6360200	Weak transcription	Fetal Stomach	stomach
45	chr8:6342400-6360200	Weak transcription	Pancreas	Pancrea
46	chr8:6342400-6360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:6342400-6360400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr8:6342400-6360400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr8:6342400-6360400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr8:6342400-6360400	Weak transcription	Rectal Mucosa Donor 29	rectum

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