Variant report

Variant	rs3130355
Chromosome Location	chr6:30318327-30318328
allele	A/G
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	SPI1	chr6:30318085-30318336	GM12891	blood:	n/a	n/a
2	SPI1	chr6:30318022-30318432	HL-60	blood:	n/a	n/a
3	RUNX3	chr6:30318236-30318700	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30178310..30184484-chr6:30311860..30320436,13	MCF-7	breast:

Variant related genes	Relation type
HLA-N	TF binding region
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11158	0.83[EUR][1000 genomes]
rs1573296	0.81[EUR][1000 genomes]
rs1970	0.81[EUR][1000 genomes]
rs2106072	0.83[EUR][1000 genomes]
rs2157678	0.81[EUR][1000 genomes]
rs2517609	0.90[EUR][1000 genomes]
rs2517617	0.90[EUR][1000 genomes]
rs2517622	0.83[EUR][1000 genomes]
rs2523712	0.90[EUR][1000 genomes]
rs2523729	0.83[EUR][1000 genomes]
rs2844777	0.93[EUR][1000 genomes]
rs3094054	0.98[EUR][1000 genomes]
rs3094056	0.98[EUR][1000 genomes]
rs3094057	0.98[EUR][1000 genomes]
rs3094058	0.98[EUR][1000 genomes]
rs3094064	1.00[EUR][1000 genomes]
rs3094066	0.96[EUR][1000 genomes]
rs3094067	1.00[EUR][1000 genomes]
rs3094069	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3094078	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3094620	0.98[EUR][1000 genomes]
rs3094621	0.87[EUR][1000 genomes]
rs3094622	0.87[EUR][1000 genomes]
rs3094624	0.98[EUR][1000 genomes]
rs3094625	0.98[EUR][1000 genomes]
rs3094628	0.91[EUR][1000 genomes]
rs3129815	0.98[EUR][1000 genomes]
rs3129830	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130350	0.98[EUR][1000 genomes]
rs3130351	0.98[EUR][1000 genomes]
rs3130352	0.98[EUR][1000 genomes]
rs3130353	0.98[EUR][1000 genomes]
rs3130363	0.85[EUR][1000 genomes]
rs3130364	0.98[EUR][1000 genomes]
rs3130377	0.98[EUR][1000 genomes]
rs3130380	0.96[EUR][1000 genomes]
rs3130399	0.96[EUR][1000 genomes]
rs3132647	0.98[EUR][1000 genomes]
rs3132648	0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130355	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30313400-30321400	Weak transcription	Spleen	Spleen
2	chr6:30313800-30325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:30314000-30318400	Weak transcription	HSMM	muscle
4	chr6:30314000-30319400	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:30314000-30319400	Weak transcription	Colonic Mucosa	Colon
6	chr6:30314000-30323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:30314000-30323200	Weak transcription	Aorta	Aorta
8	chr6:30314000-30324200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:30314000-30325600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:30314200-30322200	Weak transcription	Fetal Brain Male	brain
11	chr6:30314200-30323400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:30314200-30325600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:30314200-30325600	Weak transcription	Psoas Muscle	Psoas
14	chr6:30314400-30319200	Weak transcription	Right Ventricle	heart
15	chr6:30314400-30325000	Weak transcription	Esophagus	oesophagus
16	chr6:30314400-30325400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:30314600-30325600	Weak transcription	Pancreas	Pancrea
18	chr6:30314800-30319000	Weak transcription	HSMMtube	muscle
19	chr6:30314800-30319400	Weak transcription	NHLF	lung
20	chr6:30315000-30318800	Weak transcription	HMEC	breast
21	chr6:30315000-30318800	Weak transcription	K562	blood
22	chr6:30315000-30320400	Weak transcription	NHDF-Ad	bronchial
23	chr6:30315000-30323200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:30315000-30323400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:30315000-30325600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:30315000-30325600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:30315000-30325600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:30315000-30325600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:30315200-30318400	Weak transcription	Placenta	Placenta
30	chr6:30315200-30318800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:30315200-30320400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:30315200-30323200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:30315400-30318600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:30315400-30318600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:30315400-30323200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:30315600-30318400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:30315600-30318600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:30315600-30318600	Weak transcription	Brain Anterior Caudate	brain
39	chr6:30315600-30318800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:30315600-30318800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:30315600-30318800	Weak transcription	Dnd41	blood
42	chr6:30315600-30319000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:30315600-30320200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:30315600-30320400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:30315600-30323200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:30315600-30324400	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:30315600-30325400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:30315600-30325400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:30315800-30318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:30315800-30324200	Weak transcription	Fetal Intestine Large	intestine

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