Variant report

Variant	rs10799491
Chromosome Location	chr1:224339423-224339424
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224307124..224309430-chr1:224336604..224339479,2	MCF-7	breast:
2	chr1:224336874..224339607-chr1:224370403..224372405,2	K562	blood:
3	chr1:224339407..224345322-chr1:224346058..224350848,8	K562	blood:
4	chr1:224338611..224340755-chr1:224369526..224371703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10799507	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10799543	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10916414	0.90[AMR][1000 genomes]
rs10916458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs10916462	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10916472	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10916497	0.80[EUR][1000 genomes]
rs12082619	0.80[EUR][1000 genomes]
rs12083770	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12120308	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12124547	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12126765	0.83[EUR][1000 genomes]
rs12126815	1.00[CEU][hapmap]
rs12133599	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12138866	0.87[EUR][1000 genomes]
rs12140137	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12184283	0.80[EUR][1000 genomes]
rs45583539	0.87[EUR][1000 genomes]
rs60256604	0.84[EUR][1000 genomes]
rs6660194	0.84[EUR][1000 genomes]
rs6686449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6694451	1.00[CEU][hapmap]
rs72753956	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753969	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753994	0.84[EUR][1000 genomes]
rs72754000	0.87[EUR][1000 genomes]
rs72754001	0.80[EUR][1000 genomes]
rs72755905	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7514140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552239	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1792939	chr1:224336636-224351023	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10799491	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
3	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:224320200-224344800	Weak transcription	Gastric	stomach
5	chr1:224320200-224345000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:224320200-224345000	Weak transcription	HUVEC	blood vessel
7	chr1:224320400-224344800	Weak transcription	Small Intestine	intestine
8	chr1:224320400-224345000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:224320400-224345000	Weak transcription	Right Ventricle	heart
10	chr1:224320400-224345200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:224320600-224344000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:224320600-224345000	Weak transcription	Pancreas	Pancrea
13	chr1:224320600-224345200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:224320800-224343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:224320800-224344200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:224320800-224344800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:224320800-224345200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:224321000-224343200	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:224321000-224343400	Weak transcription	Fetal Brain Male	brain
20	chr1:224321000-224344200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:224321000-224344800	Weak transcription	NHLF	lung
22	chr1:224321000-224345000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:224321000-224345400	Weak transcription	Fetal Heart	heart
24	chr1:224322000-224345400	Weak transcription	HMEC	breast
25	chr1:224322600-224345000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:224323000-224341000	Weak transcription	NH-A	brain
27	chr1:224323000-224343200	Weak transcription	NHDF-Ad	bronchial
28	chr1:224324200-224343800	Weak transcription	HepG2	liver
29	chr1:224325000-224351000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:224326200-224345200	Weak transcription	Colonic Mucosa	Colon
31	chr1:224326800-224344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:224327000-224340200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:224327000-224345000	Weak transcription	GM12878-XiMat	blood
34	chr1:224327200-224341000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:224327400-224343200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:224327400-224343400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:224327400-224344000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:224327600-224340200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:224327600-224340800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:224327600-224356400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:224327800-224341400	Weak transcription	Lung	lung
42	chr1:224327800-224344000	Weak transcription	Left Ventricle	heart
43	chr1:224327800-224345000	Weak transcription	Aorta	Aorta
44	chr1:224327800-224345000	Weak transcription	Esophagus	oesophagus
45	chr1:224328000-224343600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:224328000-224344600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:224328200-224340200	Weak transcription	HSMM	muscle
48	chr1:224328200-224341200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:224328200-224343400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:224328200-224343800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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