Variant report

Variant	rs2632412
Chromosome Location	chr4:95149319-95149320
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95127424..95132801-chr4:95147153..95153356,7	K562	blood:

Variant related genes	Relation type
ENSG00000163104	Chromatin interaction
ENSG00000246541	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10016806	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10024642	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10028613	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10030586	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10034781	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10856908	0.84[EUR][1000 genomes]
rs10856909	0.90[MEX][hapmap]
rs11097408	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11097417	0.90[MEX][hapmap]
rs11722476	0.85[GIH][hapmap]
rs12511433	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12646184	0.85[GIH][hapmap]
rs13111083	0.84[EUR][1000 genomes]
rs13434570	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13435702	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1509946	0.92[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1565062	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17021463	0.83[EUR][1000 genomes]
rs17309887	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs183993	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2087170	0.83[GIH][hapmap]
rs2276910	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2632401	0.85[GIH][hapmap]
rs2632405	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2632410	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2632411	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2632417	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2664871	0.85[GIH][hapmap]
rs2664872	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2664880	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2664881	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2664894	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs282447	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs282450	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2865345	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2865350	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2883	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3106134	0.85[GIH][hapmap]
rs3113863	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4235050	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4558832	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4693003	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4693004	0.85[GIH][hapmap]
rs4693376	0.95[CEU][hapmap]
rs4693378	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4693381	0.95[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs62320427	0.85[ASN][1000 genomes]
rs6532476	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs6823404	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs6840674	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6841121	0.85[EUR][1000 genomes]
rs6855358	0.80[EUR][1000 genomes]
rs7439869	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7657789	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7676797	0.85[ASN][1000 genomes]
rs7685121	0.95[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7697827	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026	0.85[GIH][hapmap]
rs8336	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9884209	0.83[EUR][1000 genomes]
rs9884431	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv1850963	chr4:95146281-95175682	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2632412	SMARCAD1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95129800-95161800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:95130000-95176000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:95130200-95162600	Weak transcription	Pancreas	Pancrea
4	chr4:95130200-95162600	Weak transcription	Small Intestine	intestine
5	chr4:95130200-95164000	Weak transcription	Spleen	Spleen
6	chr4:95130200-95193000	Weak transcription	Right Ventricle	heart
7	chr4:95130200-95194000	Weak transcription	Gastric	stomach
8	chr4:95130200-95198200	Weak transcription	Colonic Mucosa	Colon
9	chr4:95130400-95152000	Weak transcription	Brain Angular Gyrus	brain
10	chr4:95130600-95151600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:95131200-95164400	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:95131600-95157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:95131600-95198200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:95131800-95161600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:95131800-95169200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:95134800-95162400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:95134800-95162800	Weak transcription	Hela-S3	cervix
18	chr4:95135200-95162600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:95135200-95162800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:95135800-95160200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:95136400-95157600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:95136600-95164800	Weak transcription	Fetal Brain Male	brain
23	chr4:95136600-95174400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:95136800-95162600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:95137400-95150600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:95137400-95162400	Weak transcription	Ovary	ovary
27	chr4:95137400-95162600	Weak transcription	Thymus	Thymus
28	chr4:95137400-95162800	Weak transcription	Psoas Muscle	Psoas
29	chr4:95137600-95162600	Weak transcription	Aorta	Aorta
30	chr4:95138000-95161400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:95138200-95162400	Weak transcription	HSMMtube	muscle
32	chr4:95138400-95164200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:95138800-95161600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:95138800-95214400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:95139200-95149600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:95140200-95167000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:95141000-95151800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:95141000-95151800	Weak transcription	Brain Substantia Nigra	brain
39	chr4:95141000-95164400	Weak transcription	A549	lung
40	chr4:95141200-95157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:95141600-95162200	Weak transcription	Fetal Brain Female	brain
42	chr4:95142000-95153000	Weak transcription	Fetal Stomach	stomach
43	chr4:95142000-95159400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:95142200-95151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:95142200-95152000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:95142200-95164200	Weak transcription	NHLF	lung
47	chr4:95142800-95160800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:95143200-95151800	Weak transcription	Brain Anterior Caudate	brain
49	chr4:95143400-95151800	Weak transcription	Liver	Liver
50	chr4:95143400-95162200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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