Variant report

Variant	rs9307834
Chromosome Location	chr4:76453850-76453851
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76439863..76442490-chr4:76450473..76453946,3	MCF-7	breast:
2	chr4:76435271..76437331-chr4:76452184..76454371,2	K562	blood:
3	chr4:76442203..76444511-chr4:76451481..76453969,2	MCF-7	breast:
4	chr4:76443470..76446392-chr4:76452432..76455084,2	K562	blood:

Variant related genes	Relation type
ENSG00000163743	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10009558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10018377	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs10020976	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10022673	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026125	0.85[EUR][1000 genomes]
rs10518139	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs11729106	0.81[YRI][hapmap]
rs11732511	0.81[YRI][hapmap]
rs13103482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134862	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs13137105	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1351094	0.82[YRI][hapmap]
rs1904104	0.81[YRI][hapmap]
rs28504656	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28609645	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867917	0.96[CEU][hapmap]
rs28871288	0.86[EUR][1000 genomes]
rs28877578	0.97[EUR][1000 genomes]
rs34402235	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35362134	0.87[EUR][1000 genomes]
rs35931543	0.87[EUR][1000 genomes]
rs62318629	0.86[EUR][1000 genomes]
rs62318632	0.87[EUR][1000 genomes]
rs6835573	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs6838603	0.86[EUR][1000 genomes]
rs7657576	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs7661260	0.88[ASN][1000 genomes]
rs7662152	0.96[CEU][hapmap]
rs7685936	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs7699102	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs9994735	0.96[CEU][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS 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 target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9307834	RCHY1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76440400-76454800	Weak transcription	Aorta	Aorta
2	chr4:76440400-76455200	Weak transcription	Esophagus	oesophagus
3	chr4:76440400-76456200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:76440400-76456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:76440400-76458000	Weak transcription	Spleen	Spleen
6	chr4:76440400-76458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:76440400-76466400	Weak transcription	Small Intestine	intestine
8	chr4:76440400-76473200	Weak transcription	Gastric	stomach
9	chr4:76440600-76454800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:76440600-76455400	Weak transcription	Right Ventricle	heart
11	chr4:76440800-76454800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:76440800-76455800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:76440800-76455800	Weak transcription	Thymus	Thymus
14	chr4:76440800-76456000	Weak transcription	Pancreas	Pancrea
15	chr4:76440800-76457400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:76440800-76458600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:76441000-76454400	Weak transcription	HUVEC	blood vessel
18	chr4:76441000-76456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:76441400-76456800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:76441400-76457400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:76441600-76454000	Weak transcription	Fetal Intestine Small	intestine
22	chr4:76441600-76456400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:76441600-76457400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:76441600-76457600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:76441600-76458600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:76441600-76459200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:76441800-76456800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:76441800-76458000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:76442000-76456800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:76442400-76455400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:76443000-76457600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:76443200-76456000	Weak transcription	Colonic Mucosa	Colon
33	chr4:76443200-76458800	Weak transcription	Stomach Mucosa	stomach
34	chr4:76443400-76470200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:76444400-76457400	Weak transcription	Hela-S3	cervix
36	chr4:76444400-76461000	Weak transcription	A549	lung
37	chr4:76444400-76471800	Weak transcription	Fetal Brain Male	brain
38	chr4:76444600-76454600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:76445400-76455400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr4:76445400-76456400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:76445600-76456200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:76445600-76457600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:76445800-76458600	Strong transcription	Liver	Liver
44	chr4:76446200-76458200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:76446200-76458400	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:76446200-76458400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:76446800-76456600	Strong transcription	Fetal Thymus	thymus
48	chr4:76446800-76458000	Strong transcription	Adipose Nuclei	Adipose
49	chr4:76447200-76455000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:76447200-76455800	Strong transcription	Dnd41	blood

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